Antisense modulation of microsomal triglyceride transfer protein expression

ABSTRACT

Antisense compounds, compositions and methods are provided for modulating the expression of microsomal triglyceride transfer protein. The compositions comprise antisense compounds, particularly antisense oligonucleotides, targeted to nucleic acids encoding microsomal triglyceride transfer protein. Methods of using these compounds for modulation of microsomal triglyceride transfer protein expression and for treatment of diseases associated with expression of microsomal triglyceride transfer protein are provided.

FIELD OF THE INVENTION

[0001] The present invention provides compositions and methods for modulating the expression of microsomal triglyceride transfer protein. In particular, this invention relates to compounds, particularly oligonucleotides, specifically hybridizable with nucleic acids encoding microsomal triglyceride transfer protein. Such compounds have been shown to modulate the expression of microsomal triglyceride transfer protein.

BACKGROUND OF THE INVENTION

[0002] Triglycerides are one of the most efficient storage forms of free energy. Because of their insolubility in biological fluids, their transport between cells and tissues requires that they be assembled into lipoprotein particles. Genetic disruption of the lipoprotein assembly/secretion pathway leads to several human disorders associated with malnutrition and developmental abnormalities. In contrast, patients displaying inappropriately high rates of lipoprotein production display increased risk for the development of atherosclerotic cardiovascular disease (Davis, Biochim. Biophys. Acta, 1999, 1440, 1-31).

[0003] The mammalian lipoprotein assembly/secretion pathway requires 2 components: apolipoprotein B (ApoB, an amphipathic protein) and a lipid transfer protein (microsomal triglyceride transfer protein, MTP). In the endoplasmic reticulum, ApoB has two possible metabolic fates: entrance into the lipoprotein assembly pathway within the lumen of the endoplasmic reticulum (ER), or degradation in the cytoplasm by the ubiquitin-dependent proteasome. The destiny of ApoB is determined by the relative availability of individual lipids and the level of expression of microsomal triglyceride transfer protein (Davis, Biochim. Biophys. Acta, 1999, 1440, 1-31).

[0004] Microsomal triglyceride transfer protein binds and shuttles individual lipid molecules between membranes. In particular, microsomal triglyceride transfer protein accelerates the transport of triglycerides, cholesteryl ester, and phospholipid from the ER membrane, where lipid molecules are synthesized, to developing lipoproteins within the lumen of the ER (Berriot-Varoqueaux et al., Annu. Rev. Nutr., 2000, 20, 663-697). In vitro analyses show that microsomal triglyceride transfer protein has a preference for transferring triglycerides and cholesteryl esters (Gordon and Jamil, Biochim. Biophys. Acta, 2000, 1486, 72-83).

[0005] Microsomal triglyceride transfer protein is a heterodimeric neutral lipid transfer protein found in the lumen of the endoplasmic reticulum of ApoB lipoprotein-secreting cells, predominantly hepatocytes and intestinal enterocytes, and has been recently detected in the human heart (Herrmann et al., J. Lipid Res., 1998, 39, 2432-2435). The smaller 55 kDa subunit of microsomal triglyceride transfer protein has been identified as protein disulfide isomerase (PDI) . The isomerase activity is not required for the complex to transfer lipid. The larger 97 kDa subunit is a unique polypeptide responsible for the in vitro binding and transfer of lipids (Gordon and Jamil, Biochim. Biophys. Acta, 2000, 1486, 72-83).

[0006] Sharp et al. isolated and sequenced cDNA encoding human microsomal triglyceride transfer protein. The large subunit of human microsomal triglyceride transfer protein spans about 55 kb and is situated on chromosome 4q22-24 (Sharp et al., Nature, 1993, 365, 65-69).

[0007] Karpe et al. detected a common functional G/T polymorphism 493 bp upstream from the transcriptional start point of the microsomal triglyceride transfer protein gene. The rare allele confers significantly higher transcriptional activity (Karpe et al., Arterioscler. Thromb. Vasc. Biol., 1998, 18, 756-761). The normal T/T genotype has a 25% lower 10-year risk of developing cardiovascular disease than the G/T genotype (Karpe et al., Arterioscler. Thromb. Vasc. Biol., 1998, 18, 756-761). In contrast, two other polymorphisms were discovered (−400 A/T and −164 T/C), but investigators concluded that the polymorphisms were unrelated to lipid variables or coronary heart disease (Herrmann et al., J. Lipid Res., 1998, 39, 2432-2435).

[0008] Disclosed and claimed in U.S. Pat. No. 5,595,872 are the nucleic acid sequences encoding the high molecular weight subunit of microsomal triglyceride transfer protein as well as expression vectors containing said nucleic acids. Additionally claimed are nucleotide sequences fully complementary to the microsomal triglyceride transfer protein sequences. Generally disclosed in the same patent are methods using antisense molecules for the reduction of microsomal triglyceride transfer protein expression (Wetterau et al., 1997).

[0009] Small molecule inhibitors of microsomal triglyceride transfer protein are well represented in the art. For example, Wetterau et al. used an isoindolinone piperidine derivative as an microsomal triglyceride transfer protein inhibitor to assay microsomal triglyceride transfer protein-mediated lipid transport. The molecule inhibited the production of lipoprotein in rodent models and normalized plasma lipoprotein levels in Watanabe-heritable hyperlipidemic (WHHL) rabbits, which are a model for human homozygous familial hypercholesterolemia (Wetterau et al., Science, 1998, 282, 751-754). Disclosed and claimed in U.S. Pat. No. 6,235,730 is the use of 3-piperidyl-4-oxoquinazoline derivatives, shown to inhibit microsomal triglyceride transfer protein, as therapeutic agents for hyperlipemia or arteriosclerotic diseases (Sato et al., 2001).

[0010] Elevated plasma lipid levels cause premature atherosclerosis. Studies of the role of microsomal triglyceride transfer protein in abetalipoproteinemia demonstrate that microsomal triglyceride transfer protein is required for both hepatic and intestinal apoB-containing lipoprotein production. An increase in microsomal triglyceride transfer protein protein in relation to very low density lipopotein (VLDL) production and secretion is thought to cause hyperlipoproteinemia, which is an underlying cause of cardiovascular disease (Kuriyama et al., Hepatology, 1998, 27, 557-562). These studies suggest that inhibition of microsomal triglyceride transfer protein function may be an effective strategy to prevent very low density lipoprotein (VLDL) and chylomicron assembly and to lower plasma lipid levels (Jamil et al., Proc. Natl. Acad. Sci. U.S.A., 1996, 93, 11991-11995).

[0011] Currently, there are no known therapeutic agents which effectively inhibit the synthesis of microsomal triglyceride transfer protein.

[0012] To date, investigative strategies aimed at modulating microsomal triglyceride transfer protein function have involved the use of small molecule inhibitors and gene knock-outs in mice.

[0013] Consequently, there remains a long felt need for additional agents capable of inhibiting microsomal triglyceride transfer protein function.

[0014] Antisense technology is emerging as an effective means for reducing the expression of specific gene products and may therefore prove to be uniquely useful in a number of therapeutic, diagnostic, and research applications for the modulation of microsomal triglyceride transfer protein expression.

[0015] The present invention provides compositions and methods for modulating microsomal triglyceride transfer protein expression.

SUMMARY OF THE INVENTION

[0016] The present invention is directed to compounds, particularly antisense oligonucleotides, which are targeted to a nucleic acid encoding microsomal triglyceride transfer protein, and which modulate the expression of microsomal triglyceride transfer protein. Pharmaceutical and other compositions comprising the compounds of the invention are also provided. Further provided are methods of modulating the expression of microsomal triglyceride transfer protein in cells or tissues comprising contacting said cells or tissues with one or more of the antisense compounds or compositions of the invention. Further provided are methods of treating an animal, particularly a human, suspected of having or being prone to a disease or condition associated with expression of microsomal triglyceride transfer protein by administering a therapeutically or prophylactically effective amount of one or more of the antisense compounds or compositions of the invention.

DETAILED DESCRIPTION OF THE INVENTION

[0017] The present invention employs oligomeric compounds, particularly antisense oligonucleotides, for use in modulating the function of nucleic acid molecules encoding microsomal triglyceride transfer protein, ultimately modulating the amount of microsomal triglyceride transfer protein produced. This is accomplished by providing antisense compounds which specifically hybridize with one or more nucleic acids encoding microsomal triglyceride transfer protein. As used herein, the terms “target nucleic acid” and “nucleic acid encoding microsomal triglyceride transfer protein” encompass DNA encoding microsomal triglyceride transfer protein, RNA (including pre-mRNA and mRNA) transcribed from such DNA, and also cDNA derived from such RNA. The specific hybridization of an oligomeric compound with its target nucleic acid interferes with the normal function of the nucleic acid. This modulation of function of a target nucleic acid by compounds which specifically hybridize to it is generally referred to as “antisense”. The functions of DNA to be interfered with include replication and transcription. The functions of RNA to be interfered with include all vital functions such as, for example, translocation of the RNA to the site of protein translation, translation of protein from the RNA, splicing of the RNA to yield one or more mRNA species, and catalytic activity which may be engaged in or facilitated by the RNA. The overall effect of such interference with target nucleic acid function is modulation of the expression of microsomal triglyceride transfer protein. In the context of the present invention, “modulation” means either an increase (stimulation) or a decrease (inhibition) in the expression of a gene. In the context of the present invention, inhibition is the preferred form of modulation of gene expression and mRNA is a preferred target.

[0018] It is preferred to target specific nucleic acids for antisense. “Targeting” an antisense compound to a particular nucleic acid, in the context of this invention, is a multistep process. The process usually begins with the identification of a nucleic acid sequence whose function is to be modulated. This may be, for example, a cellular gene (or mRNA transcribed from the gene) whose expression is associated with a particular disorder or disease state, or a nucleic acid molecule from an infectious agent. In the present invention, the target is a nucleic acid molecule encoding microsomal triglyceride transfer protein. The targeting process also includes determination of a site or sites within this gene for the antisense interaction to occur such that the desired effect, e.g., detection or modulation of expression of the protein, will result. Within the context of the present invention, a preferred intragenic site is the region encompassing the translation initiation or termination codon of the open reading frame (ORF) of the gene. Since, as is known in the art, the translation initiation codon is typically 5′-AUG (in transcribed mRNA molecules; 5′-ATG in the corresponding DNA molecule), the translation initiation codon is also referred to as the “AUG codon,” the “start codon” or the “AUG start codon”. A minority of genes have a translation initiation codon having the RNA sequence 5′-GUG, 5′-UUG or 5′-CUG, and 5′-AUA, 5′-ACG and 5′-CUG have been shown to function in vivo. Thus, the terms “translation initiation codon” and “start codon” can encompass many codon sequences, even though the initiator amino acid in each instance is typically methionine (in eukaryotes) or formylmethionine (in prokaryotes). It is also known in the art that eukaryotic and prokaryotic genes may have two or more alternative start codons, any one of which may be preferentially utilized for translation initiation in a particular cell type or tissue, or under a particular set of conditions. In the context of the invention, “start codon” and “translation initiation codon” refer to the codon or codons that are used in vivo to initiate translation of an MRNA molecule transcribed from a gene encoding microsomal triglyceride transfer protein, regardless of the sequence(s) of such codons.

[0019] It is also known in the art that a translation termination codon (or “stop codon”) of a gene may have one of three sequences, i.e., 5′-UAA, 5′-UAG and 5′-UGA (the corresponding DNA sequences are 5′-TAA, 5′-TAG and 5′-TGA, respectively). The terms “start codon region” and “translation initiation codon region” refer to a portion of such an mRNA or gene that encompasses from about 25 to about 50 contiguous nucleotides in either direction (i.e., 5′ or 3′) from a translation initiation codon. Similarly, the terms “stop codon region” and “translation termination codon region” refer to a portion of such an mRNA or gene that encompasses from about 25 to about 50 contiguous nucleotides in either direction (i.e., 5′ or 3′) from a translation termination codon.

[0020] The open reading frame (ORF) or “coding region,” which is known in the art to refer to the region between the translation initiation codon and the translation termination codon, is also a region which may be targeted effectively. Other target regions include the 5′ untranslated region (5′ UTR), known in the art to refer to the portion of an mRNA in the 5′ direction from the translation initiation codon, and thus including nucleotides between the 5′ cap site and the translation initiation codon of an mRNA or corresponding nucleotides on the gene, and the 31 untranslated region (3′ UTR), known in the art to refer to the portion of an mRNA in the 3′ direction from the translation termination codon, and thus including nucleotides between the translation termination codon and 3′ end of an mRNA or corresponding nucleotides on the gene. The 5′ cap of an MRNA comprises an N7-methylated guanosine residue joined to the 5′-most residue of the MRNA via a 5′-5′ triphosphate linkage. The 5′ cap region of an mRNA is considered to include the 5′ cap structure itself as well as the first 50 nucleotides adjacent to the cap. The 5′ cap region may also be a preferred target region.

[0021] Although some eukaryotic mRNA transcripts are directly translated, many contain one or more regions, known as “introns,” which are excised from a transcript before it is translated. The remaining (and therefore translated) regions are known as “exons” and are spliced together to form a continuous mRNA sequence. mRNA splice sites, i.e., intron-exon junctions, may also be preferred target regions, and are particularly useful in situations where aberrant splicing is implicated in disease, or where an overproduction of a particular mRNA splice product is implicated in disease. Aberrant fusion junctions due to rearrangements or deletions are also preferred targets. It has also been found that introns can also be effective, and therefore preferred, target regions for antisense compounds targeted, for example, to DNA or pre-mRNA.

[0022] Once one or more target sites have been identified, oligonucleotides are chosen which are sufficiently complementary to the target, i.e., hybridize sufficiently well and with sufficient specificity, to give the desired effect.

[0023] In the context of this invention, “hybridization” means hydrogen bonding, which may be Watson-Crick, Hoogsteen or reversed Hoogsteen hydrogen bonding, between complementary nucleoside or nucleotide bases. For example, adenine and thymine are complementary nucleobases which pair through the formation of hydrogen bonds. “Complementary,” as used herein, refers to the capacity for precise pairing between two nucleotides. For example, if a nucleotide at a certain position of an oligonucleotide is capable of hydrogen bonding with a nucleotide at the same position of a DNA or RNA molecule, then the oligonucleotide and the DNA or RNA are considered to be complementary to each other at that position. The oligonucleotide and the DNA or RNA are complementary to each other when a sufficient number of corresponding positions in each molecule are occupied by nucleotides which can hydrogen bond with each other. Thus, “specifically hybridizable” and “complementary” are terms which are used to indicate a sufficient degree of complementarity or precise pairing such that stable and specific binding occurs between the oligonucleotide and the DNA or RNA target. It is understood in the art that the sequence of an antisense compound need not be 100% complementary to that of its target nucleic acid to be specifically hybridizable. An antisense compound is specifically hybridizable when binding of the compound to the target DNA or RNA molecule interferes with the normal function of the target DNA or RNA to cause a loss of utility, and there is a sufficient degree of complementarity to avoid non-specific binding of the antisense compound to non-target sequences under conditions in which specific binding is desired, i.e., under physiological conditions in the case of in vivo assays or therapeutic treatment, and in the case of in vitro assays, under conditions in which the assays are performed.

[0024] Antisense and other compounds of the invention which hybridize to the target and inhibit expression of the target are identified through experimentation, and the sequences of these compounds are hereinbelow identified as preferred embodiments of the invention. The target sites to which these preferred sequences are complementary are hereinbelow referred to as “active sites” and are therefore preferred sites for targeting. Therefore another embodiment of the invention encompasses compounds which hybridize to these active sites.

[0025] Antisense compounds are commonly used as research reagents and diagnostics. For example, antisense oligonucleotides, which are able to inhibit gene expression with exquisite specificity, are often used by those of ordinary skill to elucidate the function of particular genes. Antisense compounds are also used, for example, to distinguish between functions of various members of a biological pathway. Antisense modulation has, therefore, been harnessed for research use.

[0026] For use in kits and diagnostics, the antisense compounds of the present invention, either alone or in combination with other antisense compounds or therapeutics, can be used as tools in differential and/or combinatorial analyses to elucidate expression patterns of a portion or the entire complement of genes expressed within cells and tissues.

[0027] Expression patterns within cells or tissues treated with one or more antisense compounds are compared to control cells or tissues not treated with antisense compounds and the patterns produced are analyzed for differential levels of gene expression as they pertain, for example, to disease association, signaling pathway, cellular localization, expression level, size, structure or function of the genes examined. These analyses can be performed on stimulated or unstimulated cells and in the presence or absence of other compounds which affect expression patterns.

[0028] Examples of methods of gene expression analysis known in the art include DNA arrays or microarrays (Brazma and Vilo, FEBS Lett., 2000, 480, 17-24; Celis, et al., FEBS Lett., 2000, 480, 2-16), SAGE (serial analysis of gene expression)(Madden, et al., Drug Discov. Today, 2000, 5, 415-425), READS (restriction enzyme amplification of digested cDNAs) (Prashar and Weissman, Methods Enzymol., 1999, 303, 258-72), TOGA (total gene expression analysis) (Sutcliffe, et al., Proc. Natl. Acad. Sci. U.S.A., 2000, 97, 1976-81), protein arrays and proteomics (Celis, et al., FEBS Lett., 2000, 480, 2-16; Jungblut, et al., Electrophoresis, 1999, 20, 2100-10) , expressed sequence tag (EST) sequencing (Celis, et al., FEBS Lett., 2000, 480, 2-16; Larsson, et al., J. Biotechnol., 2000, 80, 143-57), subtractive RNA fingerprinting (SuRF) (Fuchs, et al., Anal. Biochem., 2000, 286, 91-98; Larson, et al., Cytometry, 2000, 41, 203-208), subtractive cloning, differential display (DD) (Jurecic and Belmont, Curr. Opin. Microbiol., 2000, 3, 316-21), comparative genomic hybridization (Carulli, et al., J. Cell Biochem. Suppl., 1998, 31, 286-96), FISH (fluorescent in situ hybridization) techniques (Going and Gusterson, Eur. J. Cancer, 1999, 35, 1895-904) and mass spectrometry methods (reviewed in (To, Comb. Chem. High Throughput Screen, 2000, 3, 235-41).

[0029] The specificity and sensitivity of antisense is also harnessed by those of skill in the art for therapeutic uses. Antisense oligonucleotides have been employed as therapeutic moieties in the treatment of disease states in animals and man. Antisense oligonucleotide drugs, including ribozymes, have been safely and effectively administered to humans and numerous clinical trials are presently underway. It is thus established that oligonucleotides can be useful therapeutic modalities that can be configured to be useful in treatment regimes for treatment of cells, tissues and animals, especially humans.

[0030] In the context of this invention, the term “oligonucleotide” refers to an oligomer or polymer of ribonucleic acid (RNA) or deoxyribonucleic acid (DNA) or mimetics thereof. This term includes oligonucleotides composed of naturally-occurring nucleobases, sugars and covalent internucleoside (backbone) linkages as well as oligonucleotides having non-naturally-occurring portions which function similarly. Such modified or substituted oligonucleotides are often preferred over native forms because of desirable properties such as, for example, enhanced cellular uptake, enhanced affinity for nucleic acid target and increased stability in the presence of nucleases.

[0031] While antisense oligonucleotides are a preferred form of antisense compound, the present invention comprehends other oligomeric antisense compounds, including but not limited to oligonucleotide mimetics such as are described below. The antisense compounds in accordance with this invention preferably comprise from about 8 to about 50 nucleobases (i.e. from about 8 to about 50 linked nucleosides) Particularly preferred antisense compounds are antisense oligonucleotides, even more preferably those comprising from about 12 to about 30 nucleobases. Antisense compounds include ribozymes, external guide sequence (EGS) oligonucleotides (oligozymes), and other short catalytic RNAs or catalytic oligonucleotides which hybridize to the target nucleic acid and modulate its expression.

[0032] As is known in the art, a nucleoside is a base-sugar combination. The base portion of the nucleoside is normally a heterocyclic base. The two most common classes of such heterocyclic bases are the purines and the pyrimidines. Nucleotides are nucleosides that further include a phosphate group covalently linked to the sugar portion of the nucleoside. For those nucleosides that include a pentofuranosyl sugar, the phosphate group can be linked to either the 2′, 3′ or 5′ hydroxyl moiety of the sugar. In forming oligonucleotides, the phosphate groups covalently link adjacent nucleosides to one another to form a linear polymeric compound. In turn the respective ends of this linear polymeric structure can be further joined to form a circular structure, however, open linear structures are generally preferred. Within the oligonucleotide structure, the phosphate groups are commonly referred to as forming the internucleoside backbone of the oligonucleotide. The normal linkage or backbone of RNA and DNA is a 3′ to 5′ phosphodiester linkage.

[0033] Specific examples of preferred antisense compounds useful in this invention include oligonucleotides containing modified backbones or non-natural internucleoside linkages. As defined in this specification, oligonucleotides having modified backbones include those that retain a phosphorus atom in the backbone and those that do not have a phosphorus atom in the backbone. For the purposes of this specification, and as sometimes referenced in the art, modified oligonucleotides that do not have a phosphorus atom in their internucleoside backbone can also be considered to be oligonucleosides.

[0034] Preferred modified oligonucleotide backbones include, for example, phosphorothioates, chiral phosphorothioates, phosphorodithioates, phosphotriesters, aminoalkylphosphotriesters, methyl and other alkyl phosphonates including 3′-alkylene phosphonates, 5′-alkylene phosphonates and chiral phosphonates, phosphinates, phosphoramidates including 3′-amino phosphoramidate and aminoalkylphosphoramidates, thionophosphoramidates, thionoalkylphosphonates, thionoalkylphosphotriesters, selenophosphates and borano-phosphates having normal 3′-5′ linkages, 2′-5′ linked analogs of these, and those having inverted polarity wherein one or more internucleotide linkages is a 3′ to 3′, 5′ to 5′ or 2′ to 2′ linkage. Preferred oligonucleotides having inverted polarity comprise a single 3′ to 3′ linkage at the 3′-most internucleotide linkage i.e. a single inverted nucleoside residue which may be abasic (the nucleobase is missing or has a hydroxyl group in place thereof) . Various salts, mixed salts and free acid forms are also included.

[0035] Representative United States patents that teach the preparation of the above phosphorus-containing linkages include, but are not limited to, U.S. Pat. Nos.: 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,196; 5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131; 5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925; 5,519,126; 5,536,821; 5,541,306; 5,550,111; 5,563,253; 5,571,799; 5,587,361; 5,194,599; 5,565,555; 5,527,899; 5,721,218; 5,672,697 and 5,625,050, certain of which are commonly owned with this application, and each of which is herein incorporated by reference.

[0036] Preferred modified oligonucleotide backbones that do not include a phosphorus atom therein have backbones that are formed by short chain alkyl or cycloalkyl internucleoside linkages, mixed heteroatom and alkyl or cycloalkyl internucleoside linkages, or one or more short chain heteroatomic or heterocyclic internucleoside linkages. These include those having morpholino linkages (formed in part from the sugar portion of a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfone backbones; formacetyl and thioformacetyl backbones; methylene formacetyl and thioformacetyl backbones; riboacetyl backbones; alkene containing backbones; sulfamate backbones; methyleneimino and methylenehydrazino backbones; sulfonate and sulfonamide backbones; amide backbones; and others having mixed N, O, S and CH₂ component parts.

[0037] Representative United States patents that teach the preparation of the above oligonucleosides include, but are not limited to, U.S. Pat. Nos.: 5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033; 5,264,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967; 5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,610,289; 5,602,240; 5,608,046; 5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; 5,792,608; 5,646,269 and 5,677,439, certain of which are commonly owned with this application, and each of which is herein incorporated by reference.

[0038] In other preferred oligonucleotide mimetics, both the sugar and the internucleoside linkage, i.e., the backbone, of the nucleotide units are replaced with novel groups. The base units are maintained for hybridization with an appropriate nucleic acid target compound. One such oligomeric compound, an oligonucleotide mimetic that has been shown to have excellent hybridization properties, is referred to as a peptide nucleic acid (PNA). In PNA compounds, the sugar-backbone of an oligonucleotide is replaced with an amide containing backbone, in particular an aminoethylglycine backbone. The nucleobases are retained and are bound directly or indirectly to aza nitrogen atoms of the amide portion of the backbone. Representative United States patents that teach the preparation of PNA compounds include, but are not limited to, U.S. Pat. Nos.: 5,539,082; 5,714,331; and 5,719,262, each of which is herein incorporated by reference. Further teaching of PNA compounds can be found in Nielsen et al., Science, 1991, 254, 1497-1500.

[0039] Most preferred embodiments of the invention are oligonucleotides with phosphorothioate backbones and oligonucleosides with heteroatom backbones, and in particular —CH₂—NH—O—CH₂—, —CH₂—N(CH₃)—O—CH₂- [known as a methylene (methylimino) or MMI backbone], —CH₂—O—N(CH₃)—CH₂—, —CH₂—N(CH₃)—N(CH₃)—CH₂— and —O—N(CH₃)—CH₂—CH₂— [wherein the native phosphodiester backbone is represented as —O—P—O—CH₂—] of the above referenced U.S. Pat. No. 5,489,677, and the amide backbones of the above referenced U.S. Pat. No. 5,602,240. Also preferred are oligonucleotides having morpholino backbone structures of the above-referenced U.S. Pat. No. 5,034,506.

[0040] Modified oligonucleotides may also contain one or more substituted sugar moieties. Preferred oligonucleotides comprise one of the following at the 2′ position: OH; F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- or N-alkynyl; or O- alkyl O- alkyl, wherein the alkyl, alkenyl and alkynyl may be substituted or unsubstituted C₁ to C₁₀ alkyl or C₂ to C₁₀ alkenyl and alkynyl. Particularly preferred are O [(CH₂)_(n)O]_(m)CH₃, O(CH₂)_(n)OCH₃, O(CH₂)_(n)NH₂, O(CH₂)_(n)CH₃, O (CH₂)_(n)ONH₂, and O(CH₂)_(n)ON[(CH₂)_(n)CH₃)]₂, where n and m are from 1 to about 10. Other preferred oligonucleotides comprise one of the following at the 2′ position: C₁ to C₁₀ lower alkyl, substituted lower alkyl, alkenyl, alkynyl, alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH₃, OCN, Cl, Br, CN, CF₃, OCF₃, SOCH₃, SO₂CH₃, ONO₂, NO₂, N₃, NH₂, heterocycloalkyl, heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl, an RNA cleaving group, a reporter group, an intercalator, a group for improving the pharmacokinetic properties of an oligonucleotide, or a group for improving the pharmacodynamic properties of an oligonucleotide, and other substituents having similar properties. A preferred modification includes 2′-methoxyethoxy (2′—O—CH₂CH₂0CH₃, also known as 2′—O—(2-methoxyethyl) or 2′-MOE) (Martin et al., Helv. Chim. Acta, 1995, 78, 486-504) i.e., an alkoxyalkoxy group. A further preferred modification includes 2′-dimethylaminooxyethoxy, i.e., a O(CH₂)₂ON(CH₃)₂ group, also known as 2′-DMAOE, as described in examples hereinbelow, and 2′-dimethylaminoethoxyethoxy (also known in the art as 2′—O—dimethylaminoethoxyethyl or 2′ -DMAEOE), i.e., 2′ —O—CH₂—O—CH₂—N(CH₂)₂, also described in examples hereinbelow.

[0041] A further preferred modification includes Locked Nucleic Acids (LNAs) in which the 2′-hydroxyl group is linked to the 3′ or 4′ carbon atom of the sugar ring thereby forming a bicyclic sugar moiety. The linkage is preferably a methelyne (—CH₂—)_(n)group bridging the 2′ oxygen atom and the 4′ carbon atom wherein n is 1 or 2. LNAs and preparation thereof are described in WO 98/39352 and WO 99/14226.

[0042] Other preferred modifications include 2′-methoxy (2′—O—CH₃), 2′-aminopropoxy (2′-OCH₂CH₂CH₂NH₂) , 2′-allyl (2′-CH₂-CH═CH₂), 2′-O-allyl (2′-OCH₂-CH═CH₂) and 2′ -fluoro (2′-F) . The 2′-modification may be in the arabino (up) position or ribo (down) position. A preferred 2′-arabino modification is 2′-F. Similar modifications may also be made at other positions on the oligonucleotide, particularly the 3′ position of the sugar on the 31 terminal nucleotide or in 2′-5′ linked oligonucleotides and the 5′ position of 5′ terminal nucleotide. Oligonucleotides may also have sugar mimetics such as cyclobutyl moieties in place of the pentofuranosyl sugar. Representative United States patents that teach the preparation of such modified sugar structures include, but are not limited to, U.S. Pat. Nos.: 4,981,957; 5,118,800; 5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514,785; 5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909; 5,610,300; 5,627,053; 5,639,873; 5,646,265; 5,658,873; 5,670,633; 5,792,747; and 5,700,920, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference in its entirety.

[0043] Oligonucleotides may also include nucleobase (often referred to in the art simply as “ebase”) modifications or substitutions. As used herein, “unmodified” or “natural” nucleobases include the purine bases adenine (A) and guanine (G), and the pyrimidine bases thymine (T), cytosine (C) and uracil (U). Modified nucleobases include other synthetic and natural nucleobases such as 5-methylcytosine (5-me-C), 5-hydroxymethyl cytosine, xanthine, hypoxanthine, 2-aminoadenine, 6-methyl and other alkyl derivatives of adenine and guanine, 2-propyl and other alkyl derivatives of adenine and guanine, 2-thiouracil, 2-thiothymine and 2-thiocytosine, 5-halouracil and cytosine, 5-propynyl (—C═-C—CH,) uracil and cytosine and other alkynyl derivatives of pyrimidine bases, 6-azo uracil, cytosine and thymine, 5-uracil (pseudouracil), 4-thiouracil, 8-halo, 8-amino, 8-thiol, 8-thioalkyl, 8-hydroxyl and other 8-substituted adenines and guanines, 5-halo particularly 5-bromo, 5-trifluoromethyl and other 5-substituted uracils and cytosines, 7-methylguanine and 7-methyladenine, 2-F-adenine, 2-amino-adenine, 8-azaguanine and 8-azaadenine, 7-deazaguanine and 7-deazaadenine and 3-deazaguanine and 3-deazaadenine. Further modified nucleobases include tricyclic pyrimidines such as phenoxazine cytidine(1H-pyrimido[5,4-b] [1,4]benzoxazin-2(3H)-one), phenothiazine cytidine (1H-pyrimido[5,4-b] [1,4]benzothiazin-2(3H)-one), G-clamps such as a substituted phenoxazine cytidine (e.g. 9-(2-aminoethoxy)-H-pyrimido[5,4-b] [1,4]benzoxazin-2(3H)-one), carbazole cytidine (2H-pyrimido[4,5-b]indol-2-one), pyridoindole cytidine (H-pyrido[3′, 2′:4,5]pyrrolo[2,3-d]pyrimidin-2-one). Modified nucleobases may also include those in which the purine or pyrimidine base is replaced with other heterocycles, for example 7-deaza-adenine, 7-deazaguanosine, 2-aminopyridine and 2-pyridone. Further nucleobases include those disclosed in U.S. Pat. No. 3,687,808, those disclosed in The Concise Encyclopedia Of Polymer Science And Engineering, pages 858-859, Kroschwitz, J. I., ed. John Wiley & Sons, 1990, those disclosed by Englisch et al., Angewandte Chemie, International Edition, 1991, 30, 613, and those disclosed by Sanghvi, Y. S., Chapter 15, Antisense Research and Applications, pages 289-302, Crooke, S. T. and Lebleu, B., ed., CRC Press, 1993. Certain of these nucleobases are particularly useful for increasing the binding affinity of the oligomeric compounds of the invention. These include 5-substituted pyrimidines, 6-azapyrimidines and N-2, N-6 and O-6-substituted purines, including 2-aminopropyladenine, 5-propynyluracil and 5-propynylcytosine. 5-methylcytosine substitutions have been shown to increase nucleic acid duplex stability by 0.6-1.2° C. (Sanghvi, Y. S., Crooke, S. T. and Lebleu, B., eds., Antisense Research and Applications, CRC Press, Boca Raton, 1993, pp. 276-278) and are presently preferred base substitutions, even more particularly when combined with 2′-O-methoxyethyl sugar modifications.

[0044] Representative United States patents that teach the preparation of certain of the above noted modified nucleobases as well as other modified nucleobases include, but are not limited to, the above noted U.S. Pat. No. 3,687,808, as well as U.S. Pat. Nos.: 4,845,205; 5,130,302; 5,134,066; 5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,459,255; 5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121, 5,596,091; 5,614,617; 5,645,985; 5,830,653; 5,763,588; 6,005,096; and 5,681,941, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference, and U.S. Pat. No. 5,750,692, which is commonly owned with the instant application and also herein incorporated by reference.

[0045] Another modification of the oligonucleotides of the invention involves chemically linking to the oligonucleotide one or more moieties or conjugates which enhance the activity, cellular distribution or cellular uptake of the oligonucleotide. The compounds of the invention can include conjugate groups covalently bound to functional groups such as primary or secondary hydroxyl groups. Conjugate groups of the invention include intercalators, reporter molecules, polyamines, polyamides, polyethylene glycols, polyethers, groups that enhance the pharmacodynamic properties of oligomers, and groups that enhance the pharmacokinetic properties of oligomers. Typical conjugates groups include cholesterols, lipids, phospholipids, biotin, phenazine, folate, phenanthridine, anthraquinone, acridine, fluoresceins, rhodamines, coumarins, and dyes. Groups that enhance the pharmacodynamic properties, in the context of this invention, include groups that improve oligomer uptake, enhance oligomer resistance to degradation, and/or strengthen sequence-specific hybridization with RNA. Groups that enhance the pharmacokinetic properties, in the context of this invention, include groups that improve oligomer uptake, distribution, metabolism or excretion. Representative conjugate groups are disclosed in International Patent Application PCT/US92/09196, filed Oct. 23, 1992 the entire disclosure of which is incorporated herein by reference. Conjugate moieties include but are not limited to lipid moieties such as a cholesterol moiety (Letsinger et al., Proc. Natl. Acad. Sci. USA, 1989, 86, 6553-6556), cholic acid (Manoharan et al., Bioorg. Med. Chem. Let., 1994, 4, 1053-1060), a thioether, e.g., hexyl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992, 660, 306-309; Manoharan et al., Bioorg. Med. Chem. Let., 1993, 3, 2765-2770), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992, 20, 533-538), an aliphatic chain, e.g., dodecandiol or undecyl residues (Saison-Behmoaras et al., EMBO J., 1991, 10, 1111-1118; Kabanov et al., FEBS Lett., 1990, 259, 327-330; Svinarchuk et al., Biochimie, 1993, 75, 49-54), a phospholipid, e.g., di-hexadecyl-rac-glycerol or triethyl-ammonium 1,2-di-O-hexadecyl-rac-glycero-3-H-phosphonate (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654; Shea et al., Nucl. Acids Res., 1990, 18, 3777-3783), a polyamine or a polyethylene glycol chain (Manoharan et al., Nucleosides & Nucleotides, 1995, 14, 969-973), or adamantane acetic acid (Manoharan et al., Tetrahedron Lett., 1995, 36, 3651-3654), a palmityl moiety (Mishra et al., Biochim. Biophys. Acta, 1995, 1264, 229-237), or an octadecylamine or hexylamino-carbonyl-oxycholesterol moiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277, 923-937. Oligonucleotides of the invention may also be conjugated to active drug substances, for example, aspirin, warfarin, phenylbutazone, ibuprofen, suprofen, fenbufen, ketoprofen, (S)-(+)-pranoprofen, carprofen, dansylsarcosine, 2,3,5-triiodobenzoic acid, flufenamic acid, folinic acid, a benzothiadiazide, chlorothiazide, a diazepine, indomethicin, a barbiturate, a cephalosporin, a sulfa drug, an antidiabetic, an antibacterial or an antibiotic. Oligonucleotide-drug conjugates and their preparation are described in U.S. patent application Ser. No. 09/334,130 (filed Jun. 15, 1999) which is incorporated herein by reference in its entirety.

[0046] Representative United States patents that teach the preparation of such oligonucleotide conjugates include, but are not limited to, U.S. Pat. Nos.: 4,828,979; 4,948,882; 5,218,105; 5,525,465; 5,541,313; 5,545,730; 5,552,538; 5,578,717, 5,580,731; 5,580,731; 5,591,584; 5,109,124; 5,118,802; 5,138,045; 5,414,077; 5,486,603; 5,512,439; 5,578,718; 5,608,046; 4,587,044; 4,605,735; 4,667,025; 4,762,779; 4,789,737; 4,824,941; 4,835,263; 4,876,335; 4,904,582; 4,958,013; 5,082,830; 5,112,963; 5,214,136; 5,082,830; 5,112,963; 5,214,136; 5,245,022; 5,254,469; 5,258,506; 5,262,536; 5,272,250; 5,292,873; 5,317,098; 5,371,241, 5,391,723; 5,416,203, 5,451,463; 5,510,475; 5,512,667; 5,514,785; 5,565,552; 5,567,810; 5,574,142; 5,585,481; 5,587,371; 5,595,726; 5,597,696; 5,599,923; 5,599,928 and 5,688,941, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference.

[0047] It is not necessary for all positions in a given compound to be uniformly modified, and in fact more than one of the aforementioned modifications may be incorporated in a single compound or even at a single nucleoside within an oligonucleotide. The present invention also includes antisense compounds which are chimeric compounds. “Chimeric” antisense compounds or “chimeras,” in the context of this invention, are antisense compounds, particularly oligonucleotides, which contain two or more chemically distinct regions, each made up of at least one monomer unit, i.e., a nucleotide in the case of an oligonucleotide compound. These oligonucleotides typically contain at least one region wherein the oligonucleotide is modified so as to confer upon the oligonucleotide increased resistance to nuclease degradation, increased cellular uptake, and/or increased binding affinity for the target nucleic acid. An additional region of the oligonucleotide may serve as a substrate for enzymes capable of cleaving RNA:DNA or RNA:RNA hybrids. By way of example, RNase H is a cellular endonuclease which cleaves the RNA strand of an RNA:DNA duplex. Activation of RNase H, therefore, results in cleavage of the RNA target, thereby greatly enhancing the efficiency of oligonucleotide inhibition of gene expression. Consequently, comparable results can often be obtained with shorter oligonucleotides when chimeric oligonucleotides are used, compared to phosphorothioate deoxyoligonucleotides hybridizing to the same target region. Cleavage of the RNA target can be routinely detected by gel electrophoresis and, if necessary, associated nucleic acid hybridization techniques known in the art.

[0048] Chimeric antisense compounds of the invention may be formed as composite structures of two or more oligonucleotides, modified oligonucleotides, oligonucleosides and/or oligonucleotide mimetics as described above. Such compounds have also been referred to in the art as hybrids or gapmers. Representative United States patents that teach the preparation of such hybrid structures include, but are not limited to, U.S. Pat. Nos.: 5,013,830; 5,149,797; 5,220,007; 5,256,775; 5,366,878; 5,403,711; 5,491,133; 5,565,350; 5,623,065; 5,652,355; 5,652,356; and 5,700,922, certain of which are commonly owned with the instant application, and each of which is herein incorporated by reference in its entirety.

[0049] The antisense compounds used in accordance with this invention may be conveniently and routinely made through the well-known technique of solid phase synthesis. Equipment for such synthesis is sold by several vendors including, for example, Applied Biosystems (Foster City, Calif.). Any other means for such synthesis known in the art may additionally or alternatively be employed. It is well known to use similar techniques to prepare oligonucleotides such as the phosphorothioates and alkylated derivatives.

[0050] The antisense compounds of the invention are synthesized in vitro and do not include antisense compositions of biological origin, or genetic vector constructs designed to direct the in vivo synthesis of antisense molecules. The compounds of the invention may also be admixed, encapsulated, conjugated or otherwise associated with other molecules, molecule structures or mixtures of compounds, as for example, liposomes, receptor targeted molecules, oral, rectal, topical or other formulations, for assisting in uptake, distribution and/or absorption. Representative United States patents that teach the preparation of such uptake, distribution and/or absorption assisting formulations include, but are not limited to, U.S. Pat. Nos.: 5,108,921; 5,354,844; 5,416,016; 5,459,127; 5,521,291; 5,543,158; 5,547,932; 5,583,020; 5,591,721; 4,426,330; 4,534,899; 5,013,556; 5,108,921; 5,213,804; 5,227,170; 5,264,221; 5,356,633; 5,395,619; 5,416,016; 5,417,978; 5,462,854; 5,469,854; 5,512,295; 5,527,528; 5,534,259; 5,543,152; 5,556,948; 5,580,575; and 5,595,756, each of which is herein incorporated by reference.

[0051] The antisense compounds of the invention encompass any pharmaceutically acceptable salts, esters, or salts of such esters, or any other compound which, upon administration to an animal including a human, is capable of providing (directly or indirectly) the biologically active metabolite or residue thereof. Accordingly, for example, the disclosure is also drawn to prodrugs and pharmaceutically acceptable salts of the compounds of the invention, pharmaceutically acceptable salts of such prodrugs, and other bioequivalents.

[0052] The term “prodrug” indicates a therapeutic agent that is prepared in an inactive form that is converted to an active form (i.e., drug) within the body or cells thereof by the action of endogenous enzymes or other chemicals and/or conditions. In particular, prodrug versions of the oligonucleotides of the invention are prepared as SATE [(S-acetyl-2-thioethyl) phosphate] derivatives according to the methods disclosed in WO 93/24510 to Gosselin et al., published Dec. 9, 1993 or in WO 94/26764 and U.S. Pat. No. 5,770,713 to Imbach et al.

[0053] The term “pharmaceutically acceptable salts” refers to physiologically and pharmaceutically acceptable salts of the compounds of the invention: i.e., salts that retain the desired biological activity of the parent compound and do not impart undesired toxicological effects thereto.

[0054] Pharmaceutically acceptable base addition salts are formed with metals or amines, such as alkali and alkaline earth metals or organic amines. Examples of metals used as cations are sodium, potassium, magnesium, calcium, and the like. Examples of suitable amines are N,N′-dibenzylethylenediamine, chloroprocaine, choline, diethanolamine, dicyclohexylamine, ethylenediamine, N-methylglucamine, and procaine (see, for example, Berge et al., “Pharmaceutical Salts,” J. of Pharma Sci., 1977, 66, 1-19). The base addition salts of said acidic compounds are prepared by contacting the free acid form with a sufficient amount of the desired base to produce the salt in the conventional manner. The free acid form may be regenerated by contacting the salt form with an acid and isolating the free acid in the conventional manner. The free acid forms differ from their respective salt forms somewhat in certain physical properties such as solubility in polar solvents, but otherwise the salts are equivalent to their respective free acid for purposes of the present invention. As used herein, a “pharmaceutical addition salt” includes a pharmaceutically acceptable salt of an acid form of one of the components of the compositions of the invention. These include organic or inorganic acid salts of the amines. Preferred acid salts are the hydrochlorides, acetates, salicylates, nitrates and phosphates. Other suitable pharmaceutically acceptable salts are well known to those skilled in the art and include basic salts of a variety of inorganic and organic acids, such as, for example, with inorganic acids, such as for example hydrochloric acid, hydrobromic acid, sulfuric acid or phosphoric acid; with organic carboxylic, sulfonic, sulfo or phospho acids or N-substituted sulfamic acids, for example acetic acid, propionic acid, glycolic acid, succinic acid, maleic acid, hydroxymaleic acid, methylmaleic acid, fumaric acid, malic acid, tartaric acid, lactic acid, oxalic acid, gluconic acid, glucaric acid, glucuronic acid, citric acid, benzoic acid, cinnamic acid, mandelic acid, salicylic acid, 4-aminosalicylic acid, 2-phenoxybenzoic acid, 2-acetoxybenzoic acid, embonic acid, nicotinic acid or isonicotinic acid; and with amino acids, such as the 20 alpha-amino acids involved in the synthesis of proteins in nature, for example glutamic acid or aspartic acid, and also with phenylacetic acid, methanesulfonic acid, ethanesulfonic acid, 2-hydroxyethanesulfonic acid, ethane-1,2-disulfonic acid, benzenesulfonic acid, 4-methylbenzenesulfonic acid, naphthalene-2-sulfonic acid, naphthalene-1,5-disulfonic acid, 2- or 3-phosphoglycerate, glucose-6-phosphate, N-cyclohexylsulfamic acid (with the formation of cyclamates), or with other acid organic compounds, such as ascorbic acid. Pharmaceutically acceptable salts of compounds may also be prepared with a pharmaceutically acceptable cation. Suitable pharmaceutically acceptable cations are well known to those skilled in the art and include alkaline, alkaline earth, ammonium and quaternary ammonium cations. Carbonates or hydrogen carbonates are also possible.

[0055] For oligonucleotides, preferred examples of pharmaceutically acceptable salts include but are not limited to (a) salts formed with cations such as sodium, potassium, ammonium, magnesium, calcium, polyamines such as spermine and spermidine, etc.; (b) acid addition salts formed with inorganic acids, for example hydrochloric acid, hydrobromic acid, sulfuric acid, phosphoric acid, nitric acid and the like; (c) salts formed with organic acids such as, for example, acetic acid, oxalic acid, tartaric acid, succinic acid, maleic acid, fumaric acid, gluconic acid, citric acid, malic acid, ascorbic acid, benzoic acid, tannic acid, palmitic acid, alginic acid, polyglutamic acid, naphthalenesulfonic acid, methanesulfonic acid, p-toluenesulfonic acid, naphthalenedisulfonic acid, polygalacturonic acid, and the like; and (d) salts formed from elemental anions such as chlorine, bromine, and iodine.

[0056] The antisense compounds of the present invention can be utilized for diagnostics, therapeutics, prophylaxis and as research reagents and kits. For therapeutics, an animal, preferably a human, suspected of having a disease or disorder which can be treated by modulating the expression of microsomal triglyceride transfer protein is treated by administering antisense compounds in accordance with this invention. The compounds of the invention can be utilized in pharmaceutical compositions by adding an effective amount of an antisense compound to a suitable pharmaceutically acceptable diluent or carrier. Use of the antisense compounds and methods of the invention may also be useful prophylactically, e.g., to prevent or delay infection, inflammation or tumor formation, for example.

[0057] The antisense compounds of the invention are useful for research and diagnostics, because these compounds hybridize to nucleic acids encoding microsomal triglyceride transfer protein, enabling sandwich and other assays to easily be constructed to exploit this fact. Hybridization of the antisense oligonucleotides of the invention with a nucleic acid encoding microsomal triglyceride transfer protein can be detected by means known in the art. Such means may include conjugation of an enzyme to the oligonucleotide, radiolabelling of the oligonucleotide or any other suitable detection means. Kits using such detection means for detecting the level of microsomal triglyceride transfer protein in a sample may also be prepared.

[0058] The present invention also includes pharmaceutical compositions and formulations which include the antisense compounds of the invention. The pharmaceutical compositions of the present invention may be administered in a number of ways depending upon whether local or systemic treatment is desired and upon the area to be treated. Administration may be topical (including ophthalmic and to mucous membranes including vaginal and rectal delivery), pulmonary, e.g., by inhalation or insufflation of powders or aerosols, including by nebulizer; intratracheal, intranasal, epidermal and transdermal), oral or parenteral. Parenteral administration includes intravenous, intraarterial, subcutaneous, intraperitoneal or intramuscular injection or infusion; or intracranial, e.g., intrathecal or intraventricular, administration. Oligonucleotides with at least one 2′-O-methoxyethyl modification are believed to be particularly useful for oral administration.

[0059] Pharmaceutical compositions and formulations for topical administration may include transdermal patches, ointments, lotions, creams, gels, drops, suppositories, sprays, liquids and powders. Conventional pharmaceutical carriers, aqueous, powder or oily bases, thickeners and the like may be necessary or desirable. Coated condoms, gloves and the like may also be useful. Preferred topical formulations include those in which the oligonucleotides of the invention are in admixture with a topical delivery agent such as lipids, liposomes, fatty acids, fatty acid esters, steroids, chelating agents and surfactants. Preferred lipids and liposomes include neutral (e.g. dioleoylphosphatidyl DOPE ethanolamine, dimyristoylphosphatidyl choline DMPC, distearolyphosphatidyl choline) negative (e.g. dimyristoylphosphatidyl glycerol DMPG) and cationic (e.g. dioleoyltetramethylaminopropyl DOTAP and dioleoylphosphatidyl ethanolamine DOTMA). Oligonucleotides of the invention may be encapsulated within liposomes or may form complexes thereto, in particular to cationic liposomes. Alternatively, oligonucleotides may be complexed to lipids, in particular to cationic lipids. Preferred fatty acids and esters include but are not limited arachidonic acid, oleic acid, eicosanoic acid, lauric acid, caprylic acid, capric acid, myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein, dilaurin, glyceryl 1-monocaprate, 1-dodecylazacycloheptan-2-one, an acylcarnitine, an acylcholine, or a C₁-C₁₀ alkyl ester (e.g. isopropylmyristate IPM), monoglyceride, diglyceride or pharmaceutically acceptable salt thereof. Topical formulations are described in detail in U.S. patent application Ser. No. 09/315,298 filed on May 20, 1999 which is incorporated herein by reference in its entirety.

[0060] Compositions and formulations for oral administration include powders or granules, microparticulates, nanoparticulates, suspensions or solutions in water or non-aqueous media, capsules, gel capsules, sachets, tablets or minitablets. Thickeners, flavoring agents, diluents, emulsifiers, dispersing aids or binders may be desirable. Preferred oral formulations are those in which oligonucleotides of the invention are administered in conjunction with one or more penetration enhancers surfactants and chelators. Preferred surfactants include fatty acids and/or esters or salts thereof, bile acids and/or salts thereof. Preferred bile acids/salts include chenodeoxycholic acid (CDCA) and ursodeoxychenodeoxycholic acid (UDCA), cholic acid, dehydrocholic acid, deoxycholic acid, glucholic acid, glycholic acid, glycodeoxycholic acid, taurocholic acid, taurodeoxycholic acid, sodium tauro-24,25-dihydro-fusidate, sodium glycodihydrofusidate. Preferred fatty acids include arachidonic acid, undecanoic acid, oleic acid, lauric acid, caprylic acid, capric acid, myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein, dilaurin, glyceryl 1-monocaprate, 1-dodecylazacycloheptan-2-one, an acylcarnitine, an acylcholine, or a monoglyceride, a diglyceride or a pharmaceutically acceptable salt thereof (e.g. sodium). Also preferred are combinations of penetration enhancers, for example, fatty acids/salts in combination with bile acids/salts. A particularly preferred combination is the sodium salt of lauric acid, capric acid and UDCA. Further penetration enhancers include polyoxyethylene-9-lauryl ether, polyoxyethylene-20-cetyl ether. Oligonucleotides of the invention may be delivered orally in granular form including sprayed dried particles, or complexed to form micro or nanoparticles. Oligonucleotide complexing agents include poly-amino acids; polyimines; polyacrylates; polyalkylacrylates, polyoxethanes, polyalkylcyanoacrylates; cationized gelatins, albumins, starches, acrylates, polyethyleneglycols (PEG) and starches; polyalkylcyanoacrylates; DEAE-derivatized polyimines, pollulans, celluloses and starches. Particularly preferred complexing agents include chitosan, N-trimethylchitosan, poly-L-lysine, polyhistidine, polyornithine, polyspermines, protamine, polyvinylpyridine, polythiodiethylamino-methylethylene P(TDAE), polyaminostyrene (e.g. p-amino), poly(methylcyanoacrylate), poly(ethylcyanoacrylate) polym(butylcyanoacrylate), poly(isobutylcyanoacrylate), poly(isohexylcynaoacrylate), DEAE-methacrylate, DEAE-hexylacrylate, DEAE-acrylamide, DEAE-albumin and DEAE-dextran, polymethylacrylate, polyhexylacrylate, poly(D,L-lactic acid), poly(DL-lactic-co-glycolic acid (PLGA), alginate, and polyethyleneglycol (PEG). Oral formulations for oligonucleotides and their preparation are described in detail in U.S. application Ser. Nos. 08/886,829 (filed Jul. 1, 1997), 09/108,673 (filed Jul. 1, 1998), 09/256,515 (filed Feb. 23, 1999), 09/082,624 (filed May 21, 1998) and 09/315,298 (filed May 20, 1999) each of which is incorporated herein by reference in their entirety.

[0061] Compositions and formulations for parenteral, intrathecal or intraventricular administration may include sterile aqueous solutions which may also contain buffers, diluents and other suitable additives such as, but not limited to, penetration enhancers, carrier compounds and other pharmaceutically acceptable carriers or excipients.

[0062] Pharmaceutical compositions of the present invention include, but are not limited to, solutions, emulsions, and liposome-containing formulations. These compositions may be generated from a variety of components that include, but are not limited to, preformed liquids, self-emulsifying solids and self-emulsifying semisolids.

[0063] The pharmaceutical formulations of the present invention, which may conveniently be presented in unit dosage form, may be prepared according to conventional techniques well known in the pharmaceutical industry. Such techniques include the step of bringing into association the active ingredients with the pharmaceutical carrier(s) or excipient(s). In general the formulations are prepared by uniformly and intimately bringing into association the active ingredients with liquid carriers or finely divided solid carriers or both, and then, if necessary, shaping the product.

[0064] The compositions of the present invention may be formulated into any of many possible dosage forms such as, but not limited to, tablets, capsules, gel capsules, liquid syrups, soft gels, suppositories, and enemas. The compositions of the present invention may also be formulated as suspensions in aqueous, non-aqueous or mixed media. Aqueous suspensions may further contain substances which increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol and/or dextran. The suspension may also contain stabilizers.

[0065] In one embodiment of the present invention the pharmaceutical compositions may be formulated and used as foams. Pharmaceutical foams include formulations such as, but not limited to, emulsions, microemulsions, creams, jellies and liposomes. While basically similar in nature these formulations vary in the components and the consistency of the final product. The preparation of such compositions and formulations is generally known to those skilled in the pharmaceutical and formulation arts and may be applied to the formulation of the compositions of the present invention.

Emulsions

[0066] The compositions of the present invention may be prepared and formulated as emulsions. Emulsions are typically heterogenous systems of one liquid dispersed in another in the form of droplets usually exceeding 0.1 μm in diameter (Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199; Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., Volume 1, p. 245; Block in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 2, p. 335; Higuchi et al., in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 1985, p. 301). Emulsions are often biphasic systems comprising of two immiscible liquid phases intimately mixed and dispersed with each other. In general, emulsions may be either water-in-oil (w/o) or of the oil-in-water (o/w) variety. When an aqueous phase is finely divided into and dispersed as minute droplets into a bulk oily phase the resulting composition is called a water-in-oil (w/o) emulsion. Alternatively, when an oily phase is finely divided into and dispersed as minute droplets into a bulk aqueous phase the resulting composition is called an oil-in-water (o/w) emulsion. Emulsions may contain additional components in addition to the dispersed phases and the active drug which may be present as a solution in either the aqueous phase, oily phase or itself as a separate phase. Pharmaceutical excipients such as emulsifiers, stabilizers, dyes, and anti-oxidants may also be present in emulsions as needed. Pharmaceutical emulsions may also be multiple emulsions that are comprised of more than two phases such as, for example, in the case of oil-in-water-in-oil (o/w/o) and water-in-oil-in-water (w/o/w) emulsions. Such complex formulations often provide certain advantages that simple binary emulsions do not. Multiple emulsions in which individual oil droplets of an o/w emulsion enclose small water droplets constitute a w/o/w emulsion. Likewise a system of oil droplets enclosed in globules of water stabilized in an oily continuous provides an o/w/o emulsion.

[0067] Emulsions are characterized by little or no thermodynamic stability. Often, the dispersed or discontinuous phase of the emulsion is well dispersed into the external or continuous phase and maintained in this form through the means of emulsifiers or the viscosity of the formulation. Either of the phases of the emulsion may be a semisolid or a solid, as is the case of emulsion-style ointment bases and creams. Other means of stabilizing emulsions entail the use of emulsifiers that may be incorporated into either phase of the emulsion. Emulsifiers may broadly be classified into four categories: synthetic surfactants, naturally occurring emulsifiers, absorption bases, and finely dispersed solids (Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).

[0068] Synthetic surfactants, also known as surface active agents, have found wide applicability in the formulation of emulsions and have been reviewed in the literature (Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), Marcel Dekker, Inc., New York, N.Y., 1988, volume 1, p. 199). Surfactants are typically amphiphilic and comprise a hydrophilic and a hydrophobic portion. The ratio of the hydrophilic to the hydrophobic nature of the surfactant has been termed the hydrophile/lipophile balance (HLB) and is a valuable tool in categorizing and selecting surfactants in the preparation of formulations. Surfactants may be classified into different classes based on the nature of the hydrophilic group: nonionic, anionic, cationic and amphoteric (Rieger, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 285).

[0069] Naturally occurring emulsifiers used in emulsion formulations include lanolin, beeswax, phosphatides, lecithin and acacia. Absorption bases possess hydrophilic properties such that they can soak up water to form w/o emulsions yet retain their semisolid consistencies, such as anhydrous lanolin and hydrophilic petrolatum. Finely divided solids have also been used as good emulsifiers especially in combination with surfactants and in viscous preparations. These include polar inorganic solids, such as heavy metal hydroxides, nonswelling clays such as bentonite, attapulgite, hectorite, kaolin, montmorillonite, colloidal aluminum silicate and colloidal magnesium aluminum silicate, pigments and nonpolar solids such as carbon or glyceryl tristearate.

[0070] A large variety of non-emulsifying materials are also included in emulsion formulations and contribute to the properties of emulsions. These include fats, oils, waxes, fatty acids, fatty alcohols, fatty esters, humectants, hydrophilic colloids, preservatives and antioxidants (Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 335; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199).

[0071] Hydrophilic colloids or hydrocolloids include naturally occurring gums and synthetic polymers such as polysaccharides (for example, acacia, agar, alginic acid, carrageenan, guar gum, karaya gum, and tragacanth), cellulose derivatives (for example, carboxymethylcellulose and carboxypropylcellulose), and synthetic polymers (for example, carbomers, cellulose ethers, and carboxyvinyl polymers). These disperse or swell in water to form colloidal solutions that stabilize emulsions by forming strong interfacial films around the dispersed-phase droplets and by increasing the viscosity of the external phase.

[0072] Since emulsions often contain a number of ingredients such as carbohydrates, proteins, sterols and phosphatides that may readily support the growth of microbes, these formulations often incorporate preservatives. Commonly used preservatives included in emulsion formulations include methyl paraben, propyl paraben, quaternary ammonium salts, benzalkonium chloride, esters of p-hydroxybenzoic acid, and boric acid. Antioxidants are also commonly added to emulsion formulations to prevent deterioration of the formulation. Antioxidants used may be free radical scavengers such as tocopherols, alkyl gallates, butylated hydroxyanisole, butylated hydroxytoluene, or reducing agents such as ascorbic acid and sodium metabisulfite, and antioxidant synergists such as citric acid, tartaric acid, and lecithin.

[0073] The application of emulsion formulations via dermatological, oral and parenteral routes and methods for their manufacture have been reviewed in the literature (Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199). Emulsion formulations for oral delivery have been very widely used because of reasons of ease of formulation, efficacy from an absorption and bioavailability standpoint. (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245; Idson, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 199). Mineral-oil base laxatives, oil-soluble vitamins and high fat nutritive preparations are among the materials that have commonly been administered orally as o/w emulsions.

[0074] In one embodiment of the present invention, the compositions of oligonucleotides and nucleic acids are formulated as microemulsions. A microemulsion may be defined as a system of water, oil and amphiphile which is a single optically isotropic and thermodynamically stable liquid solution (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245). Typically microemulsions are systems that are prepared by first dispersing an oil in an aqueous surfactant solution and then adding a sufficient amount of a fourth component, generally an intermediate chain-length alcohol to form a transparent system. Therefore, microemulsions have also been described as thermodynamically stable, isotropically clear dispersions of two immiscible liquids that are stabilized by interfacial films of surface-active molecules (Leung and Shah, in: Controlled Release of Drugs: Polymers and Aggregate Systems, Rosoff, M., Ed., 1989, VCH Publishers, New York, pages 185-215). Microemulsions commonly are prepared via a combination of three to five components that include oil, water, surfactant, cosurfactant and electrolyte. Whether the microemulsion is of the water-in-oil (w/o) or an oil-in-water (o/w) type is dependent on the properties of the oil and surfactant used and on the structure and geometric packing of the polar heads and hydrocarbon tails of the surfactant molecules (Schott, in Remington's Pharmaceutical Sciences, Mack Publishing Co., Easton, Pa., 1985, p. 271).

[0075] The phenomenological approach utilizing phase diagrams has been extensively studied and has yielded a comprehensive knowledge, to one skilled in the art, of how to formulate microemulsions (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245; Block, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 335). Compared to conventional emulsions, microemulsions offer the advantage of solubilizing water-insoluble drugs in a formulation of thermodynamically stable droplets that are formed spontaneously.

[0076] Surfactants used in the preparation of microemulsions include, but are not limited to, ionic surfactants, non-ionic surfactants, Brij 96, polyoxyethylene oleyl ethers, polyglycerol fatty acid esters, tetraglycerol monolaurate (ML310), tetraglycerol monooleate (MO310), hexaglycerol monooleate (PO310), hexaglycerol pentaoleate (PO500), decaglycerol monocaprate (MCA750), decaglycerol monooleate (MO750), decaglycerol sequioleate (SO750), decaglycerol decaoleate (DAO750), alone or in combination with cosurfactants. The cosurfactant, usually a short-chain alcohol such as ethanol, 1-propanol, and 1-butanol, serves to increase the interfacial fluidity by penetrating into the surfactant film and consequently creating a disordered film because of the void space generated among surfactant molecules. Microemulsions may, however, be prepared without the use of cosurfactants and alcohol-free self-emulsifying microemulsion systems are known in the art. The aqueous phase may typically be, but is not limited to, water, an aqueous solution of the drug, glycerol, PEG300, PEG400, polyglycerols, propylene glycols, and derivatives of ethylene glycol. The oil phase may include, but is not limited to, materials such as Captex 300, Captex 355, Capmul MCM, fatty acid esters, medium chain (C8-C12) mono, di, and tri-glycerides, polyoxyethylated glyceryl fatty acid esters, fatty alcohols, polyglycolized glycerides, saturated polyglycolized C8-C10 glycerides, vegetable oils and silicone oil.

[0077] Microemulsions are particularly of interest from the standpoint of drug solubilization and the enhanced absorption of drugs. Lipid based microemulsions (both o/w and w/o) have been proposed to enhance the oral bioavailability of drugs, including peptides (Constantinides et al., Pharmaceutical Research, 1994, 11, 1385-1390; Ritschel, Meth. Find. Exp. Clin. Pharmacol., 1993, 13, 205). Microemulsions afford advantages of improved drug solubilization, protection of drug from enzymatic hydrolysis, possible enhancement of drug absorption due to surfactant-induced alterations in membrane fluidity and permeability, ease of preparation, ease of oral administration over solid dosage forms, improved clinical potency, and decreased toxicity (Constantinides et al., Pharmaceutical Research, 1994, 11, 1385; Ho et al., J. Pharm. Sci., 1996, 85, 138-143). Often microemulsions may form spontaneously when their components are brought together at ambient temperature. This may be particularly advantageous when formulating thermolabile drugs, peptides or oligonucleotides. Microemulsions have also been effective in the transdermal delivery of active components in both cosmetic and pharmaceutical applications. It is expected that the microemulsion compositions and formulations of the present invention will facilitate the increased systemic absorption of oligonucleotides and nucleic acids from the gastrointestinal tract, as well as improve the local cellular uptake of oligonucleotides and nucleic acids within the gastrointestinal tract, vagina, buccal cavity and other areas of administration.

[0078] Microemulsions of the present invention may also contain additional components and additives such as sorbitan monostearate (Grill 3), Labrasol, and penetration enhancers to improve the properties of the formulation and to enhance the absorption of the oligonucleotides and nucleic acids of the present invention. Penetration enhancers used in the microemulsions of the present invention may be classified as belonging to one of five broad categories—surfactants, fatty acids, bile salts, chelating agents, and non-chelating non-surfactants (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p. 92). Each of these classes has been discussed above.

Liposomes

[0079] There are many organized surfactant structures besides microemulsions that have been studied and used for the formulation of drugs. These include monolayers, micelles, bilayers and vesicles. Vesicles, such as liposomes, have attracted great interest because of their specificity and the duration of action they offer from the standpoint of drug delivery. As used in the present invention, the term “liposome” means a vesicle composed of amphiphilic lipids arranged in a spherical bilayer or bilayers.

[0080] Liposomes are unilamellar or multilamellar vesicles which have a membrane formed from a lipophilic material and an aqueous interior. The aqueous portion contains the composition to be delivered. Cationic liposomes possess the advantage of being able to fuse to the cell wall. Non-cationic liposomes, although not able to fuse as efficiently with the cell wall, are taken up by macrophages in vivo.

[0081] In order to cross intact mammalian skin, lipid vesicles must pass through a series of fine pores, each with a diameter less than 50 nm, under the influence of a suitable transdermal gradient. Therefore, it is desirable to use a liposome which is highly deformable and able to pass through such fine pores.

[0082] Further advantages of liposomes include; liposomes obtained from natural phospholipids are biocompatible and biodegradable; liposomes can incorporate a wide range of water and lipid soluble drugs; liposomes can protect encapsulated drugs in their internal compartments from metabolism and degradation (Rosoff, in Pharmaceutical Dosage Forms, Lieberman, Rieger and Banker (Eds.), 1988, Marcel Dekker, Inc., New York, N.Y., volume 1, p. 245). Important considerations in the preparation of liposome formulations are the lipid surface charge, vesicle size and the aqueous volume of the liposomes.

[0083] Liposomes are useful for the transfer and delivery of active ingredients to the site of action. Because the liposomal membrane is structurally similar to biological membranes, when liposomes are applied to a tissue, the liposomes start to merge with the cellular membranes. As the merging of the liposome and cell progresses, the liposomal contents are emptied into the cell where the active agent may act.

[0084] Liposomal formulations have been the focus of extensive investigation as the mode of delivery for many drugs. There is growing evidence that for topical administration, liposomes present several advantages over other formulations. Such advantages include reduced side-effects related to high systemic absorption of the administered drug, increased accumulation of the administered drug at the desired target, and the ability to administer a wide variety of drugs, both hydrophilic and hydrophobic, into the skin.

[0085] Several reports have detailed the ability of liposomes to deliver agents including high-molecular weight DNA into the skin. Compounds including analgesics, antibodies, hormones and high-molecular weight DNAs have been administered to the skin. The majority of applications resulted in the targeting of the upper epidermis.

[0086] Liposomes fall into two broad classes. Cationic liposomes are positively charged liposomes which interact with the negatively charged DNA molecules to form a stable complex. The positively charged DNA/liposome complex binds to the negatively charged cell surface and is internalized in an endosome. Due to the acidic pH within the endosome, the liposomes are ruptured, releasing their contents into the cell cytoplasm (Wang et al., Biochem. Biophys. Res. Commun., 1987, 147, 980-985).

[0087] Liposomes which are pH-sensitive or negatively-charged, entrap DNA rather than complex with it. Since both the DNA and the lipid are similarly charged, repulsion rather than complex formation occurs. Nevertheless, some DNA is entrapped within the aqueous interior of these liposomes. pH-sensitive liposomes have been used to deliver DNA encoding the thymidine kinase gene to cell monolayers in culture. Expression of the exogenous gene was detected in the target cells (Zhou et al., Journal of Controlled Release, 1992, 19, 269-274).

[0088] One major type of liposomal composition includes phospholipids other than naturally-derived phosphatidylcholine. Neutral liposome compositions, for example, can be formed from dimyristoyl phosphatidylcholine (DMPC) or dipalmitoyl phosphatidylcholine (DPPC). Anionic liposome compositions generally are formed from dimyristoyl phosphatidylglycerol, while anionic fusogenic liposomes are formed primarily from dioleoyl phosphatidylethanolamine (DOPE). Another type of liposomal composition is formed from phosphatidylcholine (PC) such as, for example, soybean PC, and egg PC. Another type is formed from mixtures of phospholipid and/or phosphatidylcholine and/or cholesterol.

[0089] Several studies have assessed the topical delivery of liposomal drug formulations to the skin. Application of liposomes containing interferon to guinea pig skin resulted in a reduction of skin herpes sores while delivery of interferon via other means (e.g. as a solution or as an emulsion) were ineffective (Weiner et al., Journal of Drug Targeting, 1992, 2, 405-410). Further, an additional study tested the efficacy of interferon administered as part of a liposomal formulation to the administration of interferon using an aqueous system, and concluded that the liposomal formulation was superior to aqueous administration (du Plessis et al., Antiviral Research, 1992, 18, 259-265).

[0090] Non-ionic liposomal systems have also been examined to determine their utility in the delivery of drugs to the skin, in particular systems comprising non-ionic surfactant and cholesterol. Non-ionic liposomal formulations comprising Novasome™ I (glyceryl dilaurate/cholesterol/polyoxyethylene-10-stearyl ether) and Novasome™ II (glyceryl distearate/cholesterol/polyoxyethylene-10-stearyl ether) were used to deliver cyclosporin-A into the dermis of mouse skin. Results indicated that such non-ionic liposomal systems were effective in facilitating the deposition of cyclosporin-A into different layers of the skin (Hu et al. S.T.P. Pharma. Sci., 1994, 4, 6, 466).

[0091] Liposomes also include “sterically stabilized” liposomes, a term which, as used herein, refers to liposomes comprising one or more specialized lipids that, when incorporated into liposomes, result in enhanced circulation lifetimes relative to liposomes lacking such specialized lipids. Examples of sterically stabilized liposomes are those in which part of the vesicle-forming lipid portion of the liposome (A) comprises one or more glycolipids, such as monosialoganglioside GM,1 or (B) is derivatized with one or more hydrophilic polymers, such as a polyethylene glycol (PEG) moiety. While not wishing to be bound by any particular theory, it is thought in the art that, at least for sterically stabilized liposomes containing gangliosides, sphingomyelin, or PEG-derivatized lipids, the enhanced circulation half-life of these sterically stabilized liposomes derives from a reduced uptake into cells of the reticuloendothelial system (RES) (Allen et al., FEBS Letters, 1987, 223, 42; Wu et al., Cancer Research, 1993, 53, 3765).

[0092] Various liposomes comprising one or more glycolipids are known in the art. Papahadjopoulos et al. (Ann. N.Y. Acad. Sci., 1987, 507, 64) reported the ability of monosialoganglioside GM1/ galactocerebroside sulfate and phosphatidylinositol to improve blood half-lives of liposomes. These findings were expounded upon by Gabizon et al. (Proc. Natl. Acad. Sci. U.S.A., 1988, 85, 6949). U.S. Pat. No. 4,837,028 and WO 88/04924, both to Allen et al., disclose liposomes comprising (1) sphingomyelin and (2) the ganglioside GM1 or a galactocerebroside sulfate ester. U.S. Pat. No. 5,543,152 (Webb et al.) discloses liposomes comprising sphingomyelin. Liposomes comprising 1,2-sn-dimyristoylphosphatidylcholine are disclosed in WO 97/13499 (Lim et al.).

[0093] Many liposomes comprising lipids derivatized with one or more hydrophilic polymers, and methods of preparation thereof, are known in the art. Sunamoto et al. (Bull. Chem. Soc. Jpn., 1980, 53, 2778) described liposomes comprising a nonionic detergent, 2C.₁₂15G, that contains a PEG moiety. Illum et al. (FEBS Lett., 1984, 167, 79) noted that hydrophilic coating of polystyrene particles with polymeric glycols results in significantly enhanced blood half-lives. Synthetic phospholipids modified by the attachment of carboxylic groups of polyalkylene glycols (e.g., PEG) are described by Sears (U.S. Pat. Nos. 4,426,330 and 4,534,899). Klibanov et al. (FEBS Lett., 1990, 268, 235) described experiments demonstrating that liposomes comprising phosphatidylethanolamine (PE) derivatized with PEG or PEG stearate have significant increases in blood circulation half-lives. Rlume et al. (Biochimica et Biophysica Acta, 1990, 1029, 91) extended such observations to other PEG-derivatized phospholipids, e.g., DSPE-PEG, formed from the combination of distearoylphosphatidylethanolamine (DSPE) and PEG. Liposomes having covalently bound PEG moieties on their external surface are described in European Patent No. EP 0 445 131 B1 and WO 90/04384 to Fisher. Liposome compositions containing 1-20 mole percent of PE derivatized with PEG, and methods of use thereof, are described by Woodle et al. (U.S. Pat. Nos. 5,013,556 and 5,356,633) and Martin et al. (U.S. Pat. No. 5,213,804 and European Patent No. EP 0 496 813 B1). Liposomes comprising a number of other lipid-polymer conjugates are disclosed in WO 91/05545 and U.S. Pat. No. 5,225,212 (both to Martin et al.) and in WO 94/20073 (Zalipsky et al.) Liposomes comprising PEG-modified ceramide lipids are described in WO 96/10391 (Choi et al.). U.S. Pat. Nos. 5,540,935 (Miyazaki et al.) and 5,556,948 (Tagawa et al.) describe PEG-containing liposomes that can be further derivatized with functional moieties on their surfaces.

[0094] A limited number of liposomes comprising nucleic acids are known in the art. WO 96/40062 to Thierry et al. discloses methods for encapsulating high molecular weight nucleic acids in liposomes. U.S. Pat. No. 5,264,221 to Tagawa et al. discloses protein-bonded liposomes and asserts that the contents of such liposomes may include an antisense RNA. U.S. Pat. No. 5,665,710 to Rahman et al. describes certain methods of encapsulating oligodeoxynucleotides in liposomes. WO 97/04787 to Love et al. discloses liposomes comprising antisense oligonucleotides targeted to the raf gene.

[0095] Transfersomes are yet another type of liposomes, and are highly deformable lipid aggregates which are attractive candidates for drug delivery vehicles. Transfersomes may be described as lipid droplets which are so highly deformable that they are easily able to penetrate through pores which are smaller than the droplet. Transfersomes are adaptable to the environment in which they are used, e.g. they are self-optimizing (adaptive to the shape of pores in the skin), self-repairing, frequently reach their targets without fragmenting, and often self-loading. To make transfersomes it is possible to add surface edge-activators, usually surfactants, to a standard liposomal composition. Transfersomes have been used to deliver serum albumin to the skin. The transfersome-mediated delivery of serum albumin has been shown to be as effective as subcutaneous injection of a solution containing serum albumin.

[0096] Surfactants find wide application in formulations such as emulsions (including microemulsions) and liposomes. The most common way of classifying and ranking the properties of the many different types of surfactants, both natural and synthetic, is by the use of the hydrophile/lipophile balance (HLB). The nature of the hydrophilic group (also known as the “head”) provides the most useful means for categorizing the different surfactants used in formulations (Rieger, in Pharmaceutical Dosage Forms, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).

[0097] If the surfactant molecule is not ionized, it is classified as a nonionic surfactant. Nonionic surfactants find wide application in pharmaceutical and cosmetic products and are usable over a wide range of pH values. In general their HLB values range from 2 to about 18 depending on their structure. Nonionic surfactants include nonionic esters such as ethylene glycol esters, propylene glycol esters, glyceryl esters, polyglyceryl esters, sorbitan esters, sucrose esters, and ethoxylated esters. Nonionic alkanolamides and ethers such as fatty alcohol ethoxylates, propoxylated alcohols, and ethoxylated/propoxylated block polymers are also included in this class. The polyoxyethylene surfactants are the most popular members of the nonionic surfactant class.

[0098] If the surfactant molecule carries a negative charge when it is dissolved or dispersed in water, the surfactant is classified as anionic. Anionic surfactants include carboxylates such as soaps, acyl lactylates, acyl amides of amino acids, esters of sulfuric acid such as alkyl sulfates and ethoxylated alkyl sulfates, sulfonates such as alkyl benzene sulfonates, acyl isethionates, acyl taurates and sulfosuccinates, and phosphates. The most important members of the anionic surfactant class are the alkyl sulfates and the soaps.

[0099] If the surfactant molecule carries a positive charge when it is dissolved or dispersed in water, the surfactant is classified as cationic. Cationic surfactants include quaternary ammonium salts and ethoxylated amines. The quaternary ammonium salts are the most used members of this class.

[0100] If the surfactant molecule has the ability to carry either a positive or negative charge, the surfactant is classified as amphoteric. Amphoteric surfactants include acrylic acid derivatives, substituted alkylamides, N-alkylbetaines and phosphatides.

[0101] The use of surfactants in drug products, formulations and in emulsions has been reviewed (Rieger, in Pharmaceutical Dosage Forms, Marcel Dekker, Inc., New York, N.Y., 1988, p. 285).

Penetration Enhancers

[0102] In one embodiment, the present invention employs various penetration enhancers to effect the efficient delivery of nucleic acids, particularly oligonucleotides, to the skin of animals. Most drugs are present in solution in both ionized and nonionized forms. However, usually only lipid soluble or lipophilic drugs readily cross cell membranes. It has been discovered that even non-lipophilic drugs may cross cell membranes if the membrane to be crossed is treated with a penetration enhancer. In addition to aiding the diffusion of non-lipophilic drugs across cell membranes, penetration enhancers also enhance the permeability of lipophilic drugs.

[0103] Penetration enhancers may be classified as belonging to one of five broad categories, i.e., surfactants, fatty acids, bile salts, chelating agents, and non-chelating non-surfactants (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p.92). Each of the above mentioned classes of penetration enhancers are described below in greater detail.

[0104] Surfactants: In connection with the present invention, surfactants (or “surface-active agents”) are chemical entities which, when dissolved in an aqueous solution, reduce the surface tension of the solution or the interfacial tension between the aqueous solution and another liquid, with the result that absorption of oligonucleotides through the mucosa is enhanced. In addition to bile salts and fatty acids, these penetration enhancers include, for example, sodium lauryl sulfate, polyoxyethylene-9-lauryl ether and polyoxyethylene-20-cetyl ether) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p.92); and perfluorochemical emulsions, such as FC-43. Takahashi et al., J. Pharm. Pharmacol., 1988, 40, 252).

[0105] Fatty acids: Various fatty acids and their derivatives which act as penetration enhancers include, for example, oleic acid, lauric acid, capric acid (n-decanoic acid), myristic acid, palmitic acid, stearic acid, linoleic acid, linolenic acid, dicaprate, tricaprate, monoolein (1-monooleoyl-rac-glycerol), dilaurin, caprylic acid, arachidonic acid, glycerol 1-monocaprate, 1-dodecylazacycloheptan-2-one, acylcarnitines, acylcholines, C1 10 alkyl esters thereof (e.g., methyl, isopropyl and t-butyl), and mono- and di-glycerides thereof (i.e., oleate, laurate, caprate, myristate, palmitate, stearate, linoleate, etc.) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, p.92; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; El Hariri et al., J. Pharm. Pharmacol., 1992, 44, 651-654).

[0106] Bile salts: The physiological role of bile includes the facilitation of dispersion and absorption of lipids and fat-soluble vitamins (Brunton, Chapter 38 in: Goodman & Gilman's The Pharmacological Basis of Therapeutics, 9th Ed., Hardman et al. Eds., McGraw-Hill, New York, 1996, pp. 934-935). Various natural bile salts, and their synthetic derivatives, act as penetration enhancers. Thus the term “bile salts” includes any of the naturally occurring components of bile as well as any of their synthetic derivatives. The bile salts of the invention include, for example, cholic acid (or its pharmaceutically acceptable sodium salt, sodium cholate), dehydrocholic acid (sodium dehydrocholate), deoxycholic acid (sodium deoxycholate), glucholic acid (sodium glucholate), glycholic acid (sodium glycocholate), glycodeoxycholic acid (sodium glycodeoxycholate), taurocholic acid (sodium taurocholate), taurodeoxycholic acid (sodium taurodeoxycholate), chenodeoxycholic acid (sodium chenodeoxycholate), ursodeoxycholic acid (UDCA), sodium tauro-24,25-dihydro-fusidate (STDHF), sodium glycodihydrofusidate and polyoxyethylene-9-lauryl ether (POE) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92; Swinyard, Chapter 39 In: Remington's Pharmaceutical Sciences, 18th Ed., Gennaro, ed., Mack Publishing Co., Easton, Pa., 1990, pages 782-783; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; Yamamoto et al., J. Pharm. Exp. Ther., 1992, 263, 25; Yamashita et al., J. Pharm. Sci., 1990, 79, 579-583).

[0107] Chelating Agents: Chelating agents, as used in connection with the present invention, can be defined as compounds that remove metallic ions from solution by forming complexes therewith, with the result that absorption of oligonucleotides through the mucosa is enhanced. With regards to their use as penetration enhancers in the present invention, chelating agents have the added advantage of also serving as DNase inhibitors, as most characterized DNA nucleases require a divalent metal ion for catalysis and are thus inhibited by chelating agents (Jarrett, J. Chromatogr., 1993, 618, 315-339). Chelating agents of the invention include but are not limited to disodium ethylenediaminetetraacetate (EDTA), citric acid, salicylates (e.g., sodium salicylate, 5-methoxysalicylate and homovanilate), N-acyl derivatives of collagen, laureth-9 and N-amino acyl derivatives of beta-diketones (enamines) (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92; Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33; Buur et al., J. Control Rel., 1990, 14, 43-51).

[0108] Non-chelating non-surfactants: As used herein, non-chelating non-surfactant penetration enhancing compounds can be defined as compounds that demonstrate insignificant activity as chelating agents or as surfactants but that nonetheless enhance absorption of oligonucleotides through the alimentary mucosa (Muranishi, Critical Reviews in Therapeutic Drug Carrier Systems, 1990, 7, 1-33). This class of penetration enhancers include, for example, unsaturated cyclic ureas, 1-alkyl- and 1-alkenylazacyclo-alkanone derivatives (Lee et al., Critical Reviews in Therapeutic Drug Carrier Systems, 1991, page 92); and non-steroidal anti-inflammatory agents such as diclofenac sodium, indomethacin and phenylbutazone (Yamashita et al., J. Pharm. Pharmacol., 1987, 39, 621-626).

[0109] Agents that enhance uptake of oligonucleotides at the cellular level may also be added to the pharmaceutical and other compositions of the present invention. For example, cationic lipids, such as lipofectin (Junichi et al, U.S. Pat. No. 5,705,188), cationic glycerol derivatives, and polycationic molecules, such as polylysine (Lollo et al., PCT Application WO 97/30731), are also known to enhance the cellular uptake of oligonucleotides.

[0110] Other agents may be utilized to enhance the penetration of the administered nucleic acids, including glycols such as ethylene glycol and propylene glycol, pyrrols such as 2-pyrrol, azones, and terpenes such as limonene and menthone.

Carriers

[0111] Certain compositions of the present invention also incorporate carrier compounds in the formulation. As used herein, “carrier compound” or “carrier” can refer to a nucleic acid, or analog thereof, which is inert (i.e., does not possess biological activity per se) but is recognized as a nucleic acid by in vivo processes that reduce the bioavailability of a nucleic acid having biological activity by, for example, degrading the biologically active nucleic acid or promoting its removal from circulation. The coadministration of a nucleic acid and a carrier compound, typically with an excess of the latter substance, can result in a substantial reduction of the amount of nucleic acid recovered in the liver, kidney or other extracirculatory reservoirs, presumably due to competition between the carrier compound and the nucleic acid for a common receptor. For example, the recovery of a partially phosphorothioate oligonucleotide in hepatic tissue can be reduced when it is coadministered with polyinosinic acid, dextran sulfate, polycytidic acid or 4-acetamido-4,isothiocyano-stilbene-2,2′-disulfonic acid (Miyao et al., Antisense Res. Dev., 1995, 5, 115-121; Takakura et al., Antisense & Nucl. Acid Drug Dev., 1996, 6, 177-183).

Excipients

[0112] In contrast to a carrier compound, a “pharmaceutical carrier” or “excipient” is a pharmaceutically acceptable solvent, suspending agent or any other pharmacologically inert vehicle for delivering one or more nucleic acids to an animal. The excipient may be liquid or solid and is selected, with the planned manner of administration in mind, so as to provide for the desired bulk, consistency, etc., when combined with a nucleic acid and the other components of a given pharmaceutical composition. Typical pharmaceutical carriers include, but are not limited to, binding agents (e.g., pregelatinized maize starch, polyvinylpyrrolidone or hydroxypropyl methylcellulose, etc.); fillers (e.g., lactose and other sugars, microcrystalline cellulose, pectin, gelatin, calcium sulfate, ethyl cellulose, polyacrylates or calcium hydrogen phosphate, etc.); lubricants (e.g., magnesium stearate, talc, silica, colloidal silicon dioxide, stearic acid, metallic stearates, hydrogenated vegetable oils, corn starch, polyethylene glycols, sodium benzoate, sodium acetate, etc.); disintegrants (e.g., starch, sodium starch glycolate, etc.); and wetting agents (e.g., sodium lauryl sulphate, etc.).

[0113] Pharmaceutically acceptable organic or inorganic excipient suitable for non-parenteral administration which do not deleteriously react with nucleic acids can also be used to formulate the compositions of the present invention. Suitable pharmaceutically acceptable carriers include, but are not limited to, water, salt solutions, alcohols, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.

[0114] Formulations for topical administration of nucleic acids may include sterile and non-sterile aqueous solutions, non-aqueous solutions in common solvents such as alcohols, or solutions of the nucleic acids in liquid or solid oil bases. The solutions may also contain buffers, diluents and other suitable additives. Pharmaceutically acceptable organic or inorganic excipients suitable for non-parenteral administration which do not deleteriously react with nucleic acids can be used.

[0115] Suitable pharmaceutically acceptable excipients include, but are not limited to, water, salt solutions, alcohol, polyethylene glycols, gelatin, lactose, amylose, magnesium stearate, talc, silicic acid, viscous paraffin, hydroxymethylcellulose, polyvinylpyrrolidone and the like.

Other Components

[0116] The compositions of the present invention may additionally contain other adjunct components conventionally found in pharmaceutical compositions, at their art-established usage levels. Thus, for example, the compositions may contain additional, compatible, pharmaceutically-active materials such as, for example, antipruritics, astringents, local anesthetics or anti-inflammatory agents, or may contain additional materials useful in physically formulating various dosage forms of the compositions of the present invention, such as dyes, flavoring agents, preservatives, antioxidants, opacifiers, thickening agents and stabilizers. However, such materials, when added, should not unduly interfere with the biological activities of the components of the compositions of the present invention. The formulations can be sterilized and, if desired, mixed with auxiliary agents, e.g., lubricants, preservatives, stabilizers, wetting agents, emulsifiers, salts for influencing osmotic pressure, buffers, colorings, flavorings and/or aromatic substances and the like which do not deleteriously interact with the nucleic acid(s) of the formulation.

[0117] Aqueous suspensions may contain substances which increase the viscosity of the suspension including, for example, sodium carboxymethylcellulose, sorbitol and/or dextran. The suspension may also contain stabilizers.

[0118] Certain embodiments of the invention provide pharmaceutical compositions containing (a) one or more antisense compounds and (b) one or more other chemotherapeutic agents which function by a non-antisense mechanism. Examples of such chemotherapeutic agents include but are not limited to daunorubicin, daunomycin, dactinomycin, doxorubicin, epirubicin, idarubicin, esorubicin, bleomycin, mafosfamide, ifosfamide, cytosine arabinoside, bis-chloroethylnitrosurea, busulfan, mitomycin C, actinomycin D, mithramycin, prednisone, hydroxyprogesterone, testosterone, tamoxifen, dacarbazine, procarbazine, hexamethylmelamine, pentamethylmelamine, mitoxantrone, amsacrine, chlorambucil, methylcyclohexylnitrosurea, nitrogen mustards, melphalan, cyclophosphamide, 6-mercaptopurine, 6-thioguanine, cytarabine, 5-azacytidine, hydroxyurea, deoxycoformycin, 4-hydroxyperoxycyclophosphoramide, 5-fluorouracil (5-FU), 5-fluorodeoxyuridine (5-FUdR), methotrexate (MTX), colchicine, taxol, vincristine, vinblastine, etoposide (VP-16), trimetrexate, irinotecan, topotecan, gemcitabine, teniposide, cisplatin and diethylstilbestrol (DES). See, generally, The Merck Manual of Diagnosis and Therapy, 15th Ed. 1987, pp. 1206-1228, Berkow et al., eds., Rahway, N.J. When used with the compounds of the invention, such chemotherapeutic agents may be used individually (e.g., 5-FU and oligonucleotide), sequentially (e.g., 5-FU and oligonucleotide for a period of time followed by MTX and oligonucleotide), or in combination with one or more other such chemotherapeutic agents (e.g., 5-FU, MTX and oligonucleotide, or 5-FU, radiotherapy and oligonucleotide). Anti-inflammatory drugs, including but not limited to nonsteroidal anti-inflammatory drugs and corticosteroids, and antiviral drugs, including but not limited to ribivirin, vidarabine, acyclovir and ganciclovir, may also be combined in compositions of the invention. See, generally, The Merck Manual of Diagnosis and Therapy, 15th Ed., Berkow et al., eds., 1987, Rahway, N.J., pages 2499-2506 and 46-49, respectively). Other non-antisense chemotherapeutic agents are also within the scope of this invention. Two or more combined compounds may be used together or sequentially.

[0119] In another related embodiment, compositions of the invention may contain one or more antisense compounds, particularly oligonucleotides, targeted to a first nucleic acid and one or more additional antisense compounds targeted to a second nucleic acid target. Numerous examples of antisense compounds are known in the art. Two or more combined compounds may be used together or sequentially.

[0120] The formulation of therapeutic compositions and their subsequent administration is believed to be within the skill of those in the art. Dosing is dependent on severity and responsiveness of the disease state to be treated, with the course of treatment lasting from several days to several months, or until a cure is effected or a diminution of the disease state is achieved. Optimal dosing schedules can be calculated from measurements of drug accumulation in the body of the patient. Persons of ordinary skill can easily determine optimum dosages, dosing methodologies and repetition rates. Optimum dosages may vary depending on the relative potency of individual oligonucleotides, and can generally be estimated based on EC₅₀s found to be effective in in vitro and in vivo animal models. In general, dosage is from 0.01 ug to 100 g per kg of body weight, and may be given once or more daily, weekly, monthly or yearly, or even once every 2 to 20 years. Persons of ordinary skill in the art can easily estimate repetition rates for dosing based on measured residence times and concentrations of the drug in bodily fluids or tissues. Following successful treatment, it may be desirable to have the patient undergo maintenance therapy to prevent the recurrence of the disease state, wherein the oligonucleotide is administered in maintenance doses, ranging from 0.01 ug to 100 g per kg of body weight, once or more daily, to once every 20 years.

[0121] While the present invention has been described with specificity in accordance with certain of its preferred embodiments, the following examples serve only to illustrate the invention and are not intended to limit the same.

EXAMPLES Example 1

[0122] Nucleoside Phosphoramidites for Oligonucleotide Synthesis Deoxy and 2′-alkoxy amidites

[0123] 2′-Deoxy and 2′-methoxy beta-cyanoethyldiisopropyl phosphoramidites were purchased from commercial sources (e.g. Chemgenes, Needham Mass. or Glen Research, Inc. Sterling Va.). Other 2′—O-alkoxy substituted nucleoside amidites are prepared as described in U.S. Pat. No. 5,506,351, herein incorporated by reference. For oligonucleotides synthesized using 2′-alkoxy amidites, the standard cycle for unmodified oligonucleotides was utilized, except the wait step after pulse delivery of tetrazole and base was increased to 360 seconds.

[0124] Oligonucleotides containing 5-methyl-2′-deoxycytidine (5-Me-C) nucleotides were synthesized according to published methods [Sanghvi, et. al., Nucleic Acids Research, 1993, 21, 3197-3203] using commercially available phosphoramidites (Glen Research, Sterling Va. or ChemGenes, Needham Mass.).

[0125] 2′-Fluoro Amidites

[0126] 2′-Fluorodeoxyadenosine amidites

[0127] 2′-fluoro oligonucleotides were synthesized as described previously [Kawasaki, et. al., J. Med. Chem., 1993, 36, 831-841] and U.S. Pat. No. 5,670,633, herein incorporated by reference. Briefly, the protected nucleoside N6-benzoyl-2′-deoxy-2′-fluoroadenosine was synthesized utilizing commercially available 9-beta-D-arabinofuranosyladenine as starting material and by modifying literature procedures whereby the 2′-alpha-fluoro atom is introduced by a S_(N)2-displacement of a 2′-beta-trityl group. Thus N6-benzoyl-9-beta-D-arabinofuranosyladenine was selectively protected in moderate yield as the 3′, 5′-ditetrahydropyranyl (THP) intermediate. Deprotection of the THP and N6-benzoyl groups was accomplished using standard methodologies and standard methods were used to obtain the 51-dimethoxytrityl-(DMT) and 5′-DMT-3′-phosphoramidite intermediates.

[0128] 2′-Fluorodeoxyguanosine

[0129] The synthesis of 2′-deoxy-2′-fluoroquanosine was accomplished using tetraisopropyldisiloxanyl (TPDS) protected 9-beta-D-arabinofuranosylguanine as starting material, and conversion to the intermediate diisobutyryl-arabinofuranosylguanosine. Deprotection of the TPDS group was followed by protection of the hydroxyl group with THP to give diisobutyryl di-THP protected arabinofuranosylguanine. Selective O-deacylation and triflation was followed by treatment of the crude product with fluoride, then deprotection of the THP groups. Standard methodologies were used to obtain the 5′-DMT- and 5′-DMT-3′-phosphoramidites.

[0130] 2′-Fluorouridine

[0131] Synthesis of 2′-deoxy-2′-fluorouridine was accomplished by the modification of a literature procedure in which 2,2′-anhydro-1-beta-D-arabinofuranosyluracil was treated with 70% hydrogen fluoride-pyridine. Standard procedures were used to obtain the 5-DMT and 5F-DMT-3′ phosphoramidites.

[0132] 2′-Fluorodeoxycytidine

[0133] 2′-deoxy-2′-fluorocytidine was synthesized via amination of 2′-deoxy-2l-fluorouridine, followed by selective protection to give N4-benzoyl-2′-deoxy-2′-fluorocytidine. Standard procedures were used to obtain the 5′-DMT and 5′-DMT-3′ phosphoramidites.

[0134] 2′-O-(2-Methoxyethyl) modified amidites

[0135] 2′-O-Methoxyethyl-substituted nucleoside amidites are prepared as follows, or alternatively, as per the methods of Martin, P., Helvetica Chimica Acta, 1995, 78, 486-504.

[0136] 2,2′-Anhydro[1-(beta-D-arabinofuranosyl)-5-methyluridine]

[0137] 5-Methyluridine (ribosylthymine, commercially available through Yamasa, Choshi, Japan) (72.0 g, 0.279 M), diphenyl-carbonate (90.0 9, 0.420 M) and sodium bicarbonate (2.0 g, 0.024 M) were added to DMF (300 mL). The mixture was heated to reflux, with stirring, allowing the evolved carbon dioxide gas to be released in a controlled manner. After 1 hour, the slightly darkened solution was concentrated under reduced pressure. The resulting syrup was poured into diethylether (2.5 L), with stirring. The product formed a gum. The ether was decanted and the residue was dissolved in a minimum amount of methanol (ca. 400 mL). The solution was poured into fresh ether (2.5 L) to yield a stiff gum. The ether was decanted and the gum was dried in a vacuum oven (60° C. at 1 mm Hg for 24 h) to give a solid that was crushed to a light tan powder (57 g, 85% crude yield). The NMR spectrum was consistent with the structure, contaminated with phenol as its sodium salt (ca. 5%). The material was used as is for further reactions (or it can be purified further by column chromatography using a gradient of methanol in ethyl acetate s(10-25%) to give a white solid, mp 222-4° C.).

[0138] 2′—O-Methoxyethyl-5-methyluridine

[0139] 2,2′-Anhydro-5-methyluridine (195 g, 0.81 M), tris(2-methoxyethyl)borate (231 g, 0.98 M) and 2-methoxyethanol (1.2 L) were added to a 2 L stainless steel pressure vessel and placed in a pre-heated oil bath at 160° C. After heating for 48 hours at 155-160° C., the vessel was opened and the solution evaporated to dryness and triturated with MeOH (200 mL). The residue was suspended in hot acetone (1 L). The insoluble salts were filtered, washed with acetone (150 mL) and the filtrate evaporated. The residue (280 g) was dissolved in CH₃CN (600 mL) and evaporated. A silica gel column (3 kg) was packed in CH₂Cl₂/acetone/MeOH (20:5:3) containing 0.5% Et₃NH. The residue was dissolved in CH₂Cl₂ (250 mL) and adsorbed onto silica (150 g) prior to loading onto the column. The product was eluted with the packing solvent to give 160 g (63%) of product. Additional material was obtained by reworking impure fractions.

[0140] 2′—O-Methoxyethyl-5-O-dimethoxytrityl-5-methyluridine

[0141] 2′—O-Methoxyethyl-5-methyluridine (160 g, 0.506 M) was co-evaporated with pyridine (250 mL) and the dried residue dissolved in pyridine (1.3 L). A first aliquot of dimethoxytrityl chloride (94.3 g, 0.278 M) was added and the mixture stirred at room temperature for one hour. A second aliquot of dimethoxytrityl chloride (94.3 g, 0.278 M) was added and the reaction stirred for an additional one hour. Methanol (170 mL) was then added to stop the reaction. HPLC showed the presence of approximately 70% product. The solvent was evaporated and triturated with CH₃CN (200 mL). The residue was dissolved in CHCl₃ (1.5 L) and extracted with 2×500 mL of saturated NaHCO₃ and 2×500 mL of saturated NaCl. The organic phase was dried over Na₂SO₄, filtered and evaporated. 275 g of residue was obtained. The residue was purified on a 3.5 kg silica gel column, packed and eluted with EtOAc/hexane/acetone (5:5:1) containing 0.5% Et₃NH. The pure fractions were evaporated to give 164 g of product. Approximately 20 g additional was obtained from the impure fractions to give a total yield of 183 g (57%).

[0142] 3′—O-Acetyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methyluridine

[0143] 2′-o-Methoxyethyl-5′—O-dimethoxytrityl-5-methyluridine (106 g, 0.167 M), DMF/pyridine (750 mL of a 3:1 mixture prepared from 562 mL of DMF and 188 mL of pyridine) and acetic anhydride (24.38 mL, 0.258 M) were combined and stirred at room temperature for 24 hours. The reaction was monitored by TLC by first quenching the TLC sample with the addition of MeOH. Upon completion of the reaction, as judged by TLC, MeOH (50 mL) was added and the mixture evaporated at 35° C. The residue was dissolved in CHCl₃ (800 mL) and extracted with 2×200 mL of saturated sodium bicarbonate and 2×200 mL of saturated NaCl. The water layers were back extracted with 200 mL of CHCl₃. The combined organics were dried with sodium sulfate and evaporated to give 122 g of residue (approx. 90% product). The residue was purified on a 3.5 kg silica gel column and eluted using EtOAc/hexane(4:1) Pure product fractions were evaporated to yield 96 g (84%). An additional 1.5 g was recovered from later fractions.

[0144] 3′—O-Acetyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methyl-4-triazoleuridine

[0145] A first solution was prepared by dissolving 3′—O-acetyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methyluridine (96 g, 0.144 M) in CH₃CN (700 mL) and set aside. Triethylamine (189 mL, 1.44 M) was added to a solution of triazole (90 g, 1.3 M) in CH₃CN (1 L), cooled to −5° C. and stirred for 0.5 h using an overhead stirrer. POC1₃ was added dropwise, over a 30 minute period, to the stirred solution maintained at 0°-10° C., and the resulting mixture stirred for an additional 2 hours. The first solution was added dropwise, over a 45 minute period, to the latter solution. The resulting reaction mixture was stored overnight in a cold room. Salts were filtered from the reaction mixture and the solution was evaporated. The residue was dissolved in EtOAc (1 L) and the insoluble solids were removed by filtration. The filtrate was washed with lx3OO mL of NaHCO₃ and 2×300 mL of saturated NaCl, dried over sodium sulfate and evaporated. The residue was triturated with EtOAc to give the title compound.

[0146] 2′—O-Methoxyethyl-5′—O-dimethoxytrityl-5-methylcytidine

[0147] A solution of 3′—O-acetyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methyl-4-triazoleuridine (103 g, 0.141 M) in dioxane (500 mL) and NH₄OH (30 mL) was stirred at room temperature for 2 hours. The dioxane solution was evaporated and the residue azeotroped with MeOH (2×200 mL). The residue was dissolved in MeOH (300 mL) and transferred to a 2 liter stainless steel pressure vessel. MeOH (400 mL) saturated with NH₃ gas was added and the vessel heated to 100° C. for 2 hours (TLC showed complete conversion). The vessel contents were evaporated to dryness and the residue was dissolved in EtOAc (500 mL) and washed once with saturated NaCl (200 mL). The organics were dried over sodium sulfate and the solvent was evaporated to give 85 g (95%) of the title compound.

[0148] N4-Benzoyl-2′-O-methoxyethyl-5′-O-dimethoxytrityl-5-methylcytidine

[0149] 2′-O-Methoxyethyl-5′-O-dimethoxytrityl-5-methylcytidine (85 g, 0.134 M) was dissolved in DMF (800 mL) and benzoic anhydride (37.2 g, 0.165 M) was added with stirring. After stirring for 3 hours, TLC showed the reaction to be approximately 95% complete. The solvent was evaporated and the residue azeotroped with MeOH (200 mL). The residue was dissolved in CHC1₃ (700 mL) and extracted with saturated NaHCO₃ (2×300 mL) and saturated NaCl (2×300 mL), dried over MgSO₄ and evaporated to give a residue (96 g). The residue was chromatographed on a 1.5 kg silica column using EtOAc/hexane (1:1) containing 0.5% Et₃NH as the eluting solvent. The pure product fractions were evaporated to give 90 g (90%) of the title compound.

[0150] N4-Benzoyl-2I—O-methoxyethyl-5′—O-dimethoxytrityl-5-methylcytidine-3′-amidite

[0151] N4-Benzoyl-2′-O-methoxyethyl-5¹-O-dimethoxytrityl-5-methylcytidine (74 g, 0.10 M) was dissolved in CH₂Cl₂ (1 L). Tetrazole diisopropylamine (7.1 g) and 2-cyanoethoxy-tetra-(isopropyl)phosphite (40.5 mL, 0.123 M) were added with stirring, under a nitrogen atmosphere. The resulting mixture was stirred for 20 hours at room temperature (TLC showed the reaction to be 95% complete). The reaction mixture was extracted with saturated NaHCO₃ (1×300 mL) and saturated NaCl (3×300 mL). The aqueous washes were back-extracted with CH₂Cl₂ (300 mL), and the extracts were combined, dried over MgSO₄ and concentrated. The residue obtained was chromatographed on a 1.5 kg silica column using EtOAc/hexane (3:1) as the eluting solvent. The pure fractions were combined to give 90.6 9 (87%) of the title compound.

[0152] 2′-O-(Aminooxyethyl) Nucleoside Amidites and 2′-O-(Dimethylaminooxyethyl) Nucleoside Amidites

[0153] 2′-(Dimethylaminooxyethoxy) nucleoside amidites

[0154] 2′-(Dimethylaminooxyethoxy) nucleoside amidites [also known in the art as 2′-O-(dimethylaminooxyethyl) nucleoside amidites] are prepared as described in the following paragraphs. Adenosine, cytidine and guanosine nucleoside amidites are prepared similarly to the thymidine (5-methyluridine) except the exocyclic amines are protected with a benzoyl moiety in the case of adenosine and cytidine and with isobutyryl in the case of guanosine.

[0155] 5′′-O-tert-Butyldiphenylsilyl-O²-2′-anhydro-5-methyluridine

[0156] O₂-2′-anhydro-5-methyluridine (Pro. Bio. Sint., Varese, Italy, 100.0 g, 0.416 mmol), dimethylaminopyridine (0.66 g, 0.013eq, 0.0054 mmol) were dissolved in dry pyridine (500 ml) at ambient temperature under an argon atmosphere and with mechanical stirring. tert-Butyldiphenylchlorosilane (125.8 g, 119.0 mL, 1.1 eq, 0.458 mmol) was added in one portion. The reaction was stirred for 16 h at ambient temperature. TLC (Rf 0.22, ethyl acetate) indicated a complete reaction. The solution was concentrated under reduced pressure to a thick oil. This was partitioned between dichloromethane (1 L) and saturated sodium bicarbonate (2×1 L) and brine (1 L). The organic layer was dried over sodium sulfate and concentrated under reduced pressure to a thick oil. The oil was dissolved in a 1:1 mixture of ethyl acetate and ethyl ether (600 mL) and the solution was cooled to −10° C. The resulting crystalline product was collected by filtration, washed with ethyl ether (3×200 mL) and dried (40° C., 1 mm Hg, 24 h) to 149 g (74.86) of white solid. TLC and NMR were consistent with pure product.

[0157] 5′-O-tert-Butyldiphenylsilyl-2′-O-(2-hydroxyethyl)-5-methyluridine

[0158] In a 2 L stainless steel, unstirred pressure reactor was added borane in tetrahydrofuran (1.0 M, 2.0 eq, 622 mL). In the fume hood and with manual stirring, ethylene glycol (350 mL, excess) was added cautiously at first until the evolution of hydrogen gas subsided. 5′-O-tert-Butyldiphenylsilyl-O²-2′-anhydro-5-methyluridine (149 g, 0.311 mol) and sodium bicarbonate (0.074 9, 0.003 eq) were added with manual stirring. The reactor was sealed and heated in an oil bath until an internal temperature of 160 ° C. was reached and then maintained for 16 h (pressure <100 psig). The reaction vessel was cooled to ambient and opened. TLC (Rf 0.67 for desired product and Rf 0.82 for ara-T side product, ethyl acetate) indicated about 70% conversion to the product. In order to avoid additional side product formation, the reaction was stopped, concentrated under reduced pressure (10 to 1 mm Hg) in a warm water bath (40-100° C.) with the more extreme conditions used to remove the ethylene glycol. [Alternatively, once the low boiling solvent is gone, the remaining solution can be partitioned between ethyl acetate and water. The product will be in the organic phase.] The residue was purified by column chromatography (2 kg silica gel, ethyl acetate-hexanes gradient 1:1 to 4:1). The appropriate fractions were combined, stripped and dried to product as a white crisp foam (84 g, 50%), contaminated starting material (17.4 g) and pure reusable starting material 20 g. The yield based on starting material less pure recovered starting material was 58%. TLC and NMR were consistent with 99% pure product.

[0159] 2′-O-([2-phthalimidoxy)ethyl]-5′-t-butyldiphenylsilyl-5-methyluridine

[0160] 5′-O-tert-Butyldiphenylsilyl-2′-O-(2-hydroxyethyl)-5-methyluridine (20 g, 36.98 mmol) was mixed with triphenylphosphine (11.63 g, 44.36 mmol) and N-hydroxyphthalimide (7.24 g, 44.36 mmol). It was then dried over P₂O₅ under high vacuum for two days at 40° C. The reaction mixture was flushed with argon and dry THF (369.8 mL, Aldrich, sure seal bottle) was added to get a clear solution. Diethyl-azodicarboxylate (6.98 mL, 44.36 mmol) was added dropwise to the reaction mixture. The rate of addition is maintained such that resulting deep red coloration is just discharged before adding the next drop. After the addition was complete, the reaction was stirred for 4 hrs. By that time TLC showed the completion of the reaction (ethylacetate:hexane, 60:40). The solvent was evaporated in vacuum. Residue obtained was placed on a flash column and eluted with ethyl acetate:hexane (60:40), to get 2′-O-([2-phthalimidoxy)ethyl]-5′-t-butyldiphenylsilyl-5-methyluridine as white foam (21.819 g, 86%).

[0161] 5′-O-tert-butyldiphenylsilyl-2′-O-[(2-formadoximinooxy)ethyl]-5-methyluridine

[0162] 2′-O-([2-phthalimidoxy)ethyl]-5′-t-butyldiphenylsilyl-5-methyluridine (3.1 g, 4.5 mmol) was dissolved in dry CH₂Cl₂ (4.5 mL) and methylhydrazine (300 mL, 4.64 mmol) was added dropwise at −10° C. to 0° C. After 1 h the mixture was filtered, the filtrate was washed with ice cold CH₂Cl₂ and the combined organic phase was washed with water, brine and dried over anhydrous Na₂SO₄. The solution was concentrated to get 2′-O-(aminooxyethyl) thymidine, which was then dissolved in MeOH (67.5 mL). To this formaldehyde (20% aqueous solution, w/w, 1.1 eq.) was added and the resulting mixture was stirred for 1 h. Solvent was removed under vacuum; residue chromatographed to get 5′ 1-tert-butyldiphenylsilyl-2′-O-[(2-formadoximinooxy) ethyl]-5-methyluridine as white foam (1.95 g, 78%).

[0163] 5′-O-tert-Butyldiphenylsilyl-2′-O-[N,N-dimethylaminooxyethyl]-5-methyluridine

[0164] 5′-O-tert-butyldiphenylsilyl-2′-O-[(2-formadoximinooxy)ethyl]-5-methyluridine (1.77 g, 3.12 mmol) was dissolved in a solution of 1M pyridinium p-toluenesulfonate (PPTS) in dry MeOH (30.6 mL). Sodium cyanoborohydride (0.39 g, 6.13 mmol) was added to this solution at 10° C. under inert atmosphere. The reaction mixture was stirred for 10 minutes at 10° C. After that the reaction vessel was removed from the ice bath and stirred at room temperature for 2 h, the reaction monitored by TLC (5% MeOH in CH₂Cl₂). Aqueous NaHCO₃ solution (5%, 10 mL) was added and extracted with ethyl acetate (2×20 mL). Ethyl acetate phase was dried over anhydrous Na₂SO₄, evaporated to dryness. Residue was dissolved in a solution of 1M PPTS in MeOH (30.6 mL). Formaldehyde (20% w/w, 30 mL, 3.37 mmol) was added and the reaction mixture was stirred at room temperature for 10 minutes. Reaction mixture cooled to 10° C. in an ice bath, sodium cyanoborohydride (0.39 g, 6.13 mmol) was added and reaction mixture stirred at 100C for 10 minutes. After 10 minutes, the reaction mixture was removed from the ice bath and stirred at room temperature for 2 hrs. To the reaction mixture 5% NaHCO₃ (25 mL) solution was added and extracted with ethyl acetate (2×25 mL). Ethyl acetate layer was dried over anhydrous Na₂SO₄ and evaporated to dryness. The residue obtained was purified by flash column chromatography and eluted with 5% MeOH in CH₂Cl₂ to get 5′-O-tert-butyldiphenylsilyl-2′-O-[N,N-dimethylaminooxyethyl]-5-methyluridine as a white foam (14.6 g, 80%).

[0165] 2′-O-(dimethylaminooxyethyl)-5-methyluridine

[0166] Triethylamine trihydrofluoride (3.9 mL, 24.0 mmol) was dissolved in dry THF and triethylamine (1.67 mL, 12 mmol, dry, kept over KOH). This mixture of triethylamine-2HF was then added to 5′-O-tert-butyldiphenylsilyl-2′-C-[N,N-dimethylaminooxyethyl]-5-methyluridine (1.40 g, 2.4 mmol) and stirred at room temperature for 24 hrs. Reaction was monitored by TLC (5% MeOH in CH₂Cl₂). Solvent was removed under vacuum and the residue placed on a flash column and eluted with 10% MeOH in CH₂Cl₂ to get 2′-O-(dimethylaminooxyethyl)-5-methyluridine (766mg, 92.5%).

[0167] 5′ 1-O-DMT-2′-O-(dimethylaminooxyethyl)-5-methyluridine

[0168] 2′-O-(dimethylaminooxyethyl)-5-methyluridine (750 mg, 2.17 mmol) was dried over P₂C₅ under high vacuum overnight at 40° C. It was then co-evaporated with anhydrous pyridine (20 mL). The residue obtained was dissolved in pyridine (11 mL) under argon atmosphere. 4-dimethylaminopyridine (26.5 mg, 2.60 mmol), 4,4′-dimethoxytrityl chloride (880 mg, 2.60 mmol) was added to the mixture and the reaction mixture was stirred at room temperature until all of the starting material disappeared. Pyridine was removed under vacuum and the residue chromatographed and eluted with 10% MeOH in CH₂Cl₂ (containing a few drops of pyridine) to get 5′-O-DMT-2′-O-(dimethylamino-oxyethyl)-5-methyluridine (1.13 g, 80%).

[0169] 5′-O-DMT-2′-O-(2-N,N-dimethylaminooxyethyl)-S-methyluridine-3′-[(2-cyanoethyl)—N,N-diisopropylphosphoramidite]

[0170] 5′-O-DMT-2′-O-(dimethylaminooxyethyl)-5-methyluridine (1.08 g, 1.67 mmol) was co-evaporated with toluene (2OmL). To the residue N,N-diisopropylamine tetrazonide (0.29 g, 1.67 mmol) was added and dried over P₂O₅ under high vacuum overnight at 40° C. Then the reaction mixture was dissolved in anhydrous acetonitrile (8.4 mL) and 2-cyanoethyl—N,N,N¹,N²-tetraisopropylphosphoramidite (2.12 mL, 6.08 mmol) was added. The reaction mixture was stirred at ambient temperature for 4 hrs under inert atmosphere. The progress of the reaction was monitored by TLC (hexane:ethyl acetate 1:1). The solvent was evaporated, then the residue was dissolved in ethyl acetate (70 mL) and washed with 5% aqueous NaHCO₃ (40 mL). Ethyl acetate layer was dried over anhydrous Na₂SO₄ and concentrated. Residue obtained was chromatographed (ethyl acetate as eluent) to get 5′-O-DMT-2′-O-(2-N,N-dimethylaminooxyethyl)-5-methyluridine-3′-[(2-cyanoethyl)-N,N-diisopropylphosphoramidite] as a foam (1.04 g, 74.9%).

[0171] 2′-(Aminooxyethoxy) nucleoside amidites

[0172] 2′-(Aminooxyethoxy) nucleoside amidites [also known in the art as 2′-O-(aminooxyethyl) nucleoside amidites] are prepared as described in the following paragraphs. Adenosine, cytidine and thymidine nucleoside amidites are prepared similarly.

[0173] N2-isobutyryl-6-O-diphenylcarbamoyl-2′-O-(2-ethylacetyl)-5′-O-(4,4′-dimethoxytrityl)guanosine-3′-[(2-cyanoethyl)—N,N-diisopropylphosphoramidite]

[0174] The 2′-O-aminooxyethyl guanosine analog may be obtained by selective 2′-O-alkylation of diaminopurine riboside. Multigram quantities of diaminopurine riboside may be purchased from Schering AG (Berlin) to provide 2′-O-(2-ethylacetyl) diaminopurine riboside along with a minor amount of the 3′-O-isomer. 2′-O-(2-ethylacetyl) diaminopurine riboside may be resolved and converted to 2′-O-(2-ethylacetyl)guanosine by treatment with adenosine deaminase. (McGee, D. P. C., Cook, P. D., Guinosso, C. J., WO 94/02501 A1940203.) Standard protection procedures should afford 2′-O-(2-ethylacetyl)-5′-O-(4,4′-dimethoxytrityl)guanosine and 2-N-isobutyryl-6-O-diphenylcarbamoyl-2 ′-O- (2-ethylacetyl) -5-O-(4,4′-dimethoxytrityl)guanosine which may be reduced to provide 2-N-isobutyryl-6-O-diphenylcarbamoyl-2 ′-O-(2-hydroxyethyl) -5′-O-(4,4′-dimethoxytrityl) guanosine. As before the hydroxyl group may be displaced by N-hydroxyphthalimide via a Mitsunobu reaction, and the protected nucleoside may phosphitylated as usual to yield 2-N-isobutyryl-6-O-diphenylcarbamoyl-2′-O-([2-phthalmidoxyl ethyl) -5′-O-(4,4′ dimethoxytrityl)guanosine-3-[(2-cyanoethyl)-N,N-diisopropylphosphoramidite].

[0175] 2′-Dimethylaminoethoxyethoxy (2′-DMAEOE) Nucleoside Amidites

[0176] 2′-dimethylaminoethoxyethoxy nucleoside amidites (also known in the art as 2′-O-dimethylaminoethoxyethyl, i.e., 2′-O—CH₂-O—CH₂-N(CH₂)₂, or 2′-DMAEOE nucleoside amidites) are prepared as follows. Other nucleoside amidites are prepared similarly.

[0177] 2′-O-[2(2-N,N-Dimethylaminoethoxy)Ethyl]-5-Methyl Uridine

[0178] 2 [2-(Dimethylamino)ethoxy]ethanol (Aldrich, 6.66 g, 50 mmol) is slowly added to a solution of borane in tetra-hydrofuran (1 M, 10 mL, 10 mmol) with stirring in a 100 mL bomb. Hydrogen gas evolves as the solid dissolves. O₂-,2′-anhydro-5-methyluridine (1.2 g, 5 mmol), and sodium bicarbonate (2.5 mg) are added and the bomb is sealed, placed in an oil bath and heated to 155° C. for 26 hours. The bomb is cooled to room temperature and opened. The crude solution is concentrated and the residue partitioned between water (200 mL) and hexanes (200 mL). The excess phenol is extracted into the hexane layer. The aqueous layer is extracted with ethyl acetate (3×200 mL) and the combined organic layers are washed once with water, dried over anhydrous sodium sulfate and concentrated. The residue is columned on silica gel using methanol/methylene chloride 1:20 (which has 2% triethylamine) as the eluent. As the column fractions are concentrated a colorless solid forms which is collected to give the title compound as a white solid.

[0179] 5′-O-Dimethoxytrityl-2′-O-[2(2-N,N-Eimethylaminoethoxy) Ethyl)]-5-Methyl Uridine

[0180] To 0.5 g (1.3 mmol) of 2′-O-[2(2-N,N-dimethylamino-ethoxy)ethyl)]-5-methyl uridine in anhydrous pyridine (8 mL), triethylamine (0.36 mL) and dimethoxytrityl chloride (DMT-Cl, 0.87 g, 2 eq.) are added and stirred for 1 hour. The reaction mixture is poured into water (200 mL) and extracted with CH₂Cl₂ (2×200 mL). The combined CH₂Cl₂ layers are washed with saturated NaHCO₃ solution, followed by saturated NaCl solution and dried over anhydrous sodium sulfate. Evaporation of the solvent followed by silica gel chromatography using MeOH:CH₂Cl₂:Et₃N (20:1, v/v, with 1% triethylamine) gives the title compound.

[0181] 5′ 1-O-Dimethoxytrityl-2′-O-(2(2-N,N-dimethylaminoethoxy)-ethyl)]-5-methyl uridine-3′-O-(cyanoethyl—N,N-diisopropyl)phosphoramidite

[0182] Diisopropylaminotetrazolide (0.6 g) and 2-cyanoethoxy-N,N-diisopropyl phosphoramidite (1.1 mL, 2 eq.) are added to a solution of 5′-O-dimethoxytrityl-2′-O-[2(2-N,N-dimethylaminoethoxy)ethyl)]-5-methyluridine (2.17 g, 3 mmol) dissolved in CH₂Cl₂ (20 mL) under an atmosphere of argon. The reaction mixture is stirred overnight and the solvent evaporated. The resulting residue is purified by silica gel flash column chromatography with ethyl acetate as the eluent to give the title compound.

Example 2

[0183] Oligonucleotide Synthesis

[0184] Unsubstituted and substituted phosphodiester (P═O) oligonucleotides are synthesized on an automated DNA synthesizer (Applied Biosystems model 380B) using standard phosphoramidite chemistry with oxidation by iodine.

[0185] Phosphorothioates (P═S) are synthesized as for the phosphodiester oligonucleotides except the standard oxidation bottle was replaced by 0.2 M solution of 3H-1,2-benzodithiole-3-one 1,1-dioxide in acetonitrile for the stepwise thiation of the phosphite linkages. The thiation wait step was increased to 68 sec and was followed by the capping step. After cleavage from the CPG column and deblocking in concentrated ammonium hydroxide at 55° C. (18 h), the oligonucleotides were purified by precipitating twice with 2.5 volumes of ethanol from a 0.5 M NaCl solution.

[0186] Phosphinate oligonucleotides are prepared as described in U.S. Pat. No. 5,508,270, herein incorporated by reference.

[0187] Alkyl phosphonate oligonucleotides are prepared as described in U.S. Pat. No. 4,469,863, herein incorporated by reference. 3′-Deoxy-31-methylene phosphonate oligonucleotides are prepared as described in U.S. Pat. Nos. 5,610,289 or 5,625,050, herein incorporated by reference.

[0188] Phosphoramidite oligonucleotides are prepared as described in U.S. Pat. No., 5,256,775 or U.S. Pat. No. 5,366,878, herein incorporated by reference.

[0189] Alkylphosphonothioate oligonucleotides are prepared as described in published PCT applications PCT/US94/00902 and PCT/US93/06976 (published as WO 94/17093 and WO 94/02499, respectively), herein incorporated by reference.

[0190] 3′-Deoxy-3′-amino phosphoramidate oligonucleotides are prepared as described in U.S. Pat. No. 5,476,925, herein incorporated by reference.

[0191] Phosphotriester oligonucleotides are prepared as described in U.S. Pat. No. 5,023,243, herein incorporated by reference.

[0192] Borano phosphate oligonucleotides are prepared as described in U.S. Pat. Nos. 5,130,302 and 5,177,198, both herein incorporated by reference.

Example 3

[0193] Oligonucleoside Synthesis

[0194] Methylenemethylimino linked oligonucleosides, also identified as MMI linked oligonucleosides, methylenedimethyl-hydrazo linked oligonucleosides, also identified as MDH linked oligonucleosides, and methylenecarbonylamino linked oligonucleosides, also identified as amide-3 linked oligonucleosides, and methyleneaminocarbonyl linked oligo-nucleosides, also identified as amide-4 linked oligonucleosides, as well as mixed backbone compounds having, for instance, alternating MMI and P═O or P═S linkages are prepared as described in U.S. Pat. Nos. 5,378,825, 5,386,023, 5,489,677, 5,602,240 and 5,610,289, all of which are herein incorporated by reference.

[0195] Formacetal and thioformacetal linked oligonucleosides are prepared as described in U.S. Pat. Nos. 5,264,562 and 5,264,564, herein incorporated by reference.

[0196] Ethylene oxide linked oligonucleosides are prepared as described in U.S. Pat. No. 5,223,618, herein incorporated by reference.

Example 4

[0197] PNA Synthesis

[0198] Peptide nucleic acids (PNAs) are prepared in accordance with any of the various procedures referred to in Peptide Nucleic Acids (PNA): Synthesis, Properties and Potential Applications, Bioorganic & Medicinal Chemistry, 1996, 4, 5-23. They may also be prepared in accordance with U.S. Pat. Nos. 5,539,082, 5,700,922, and 5,719,262, herein incorporated by reference.

Example 5

[0199] Synthesis of Chimeric Oligonucleotides

[0200] Chimeric oligonucleotides, oligonucleosides or mixed oligonucleotides/oligonucleosides of the invention can be of several different types. These include a first type wherein the “gap” segment of linked nucleosides is positioned between 5′ and 3′ “wing” segments of linked nucleosides and a second “open end” type wherein the “gap” segment is located at either the 3′ or the 5′ terminus of the oligomeric compound. Oligonucleotides of the first type are also known in the art as “gapmers” or gapped oligonucleotides. Oligonucleotides of the second type are also known in the art as “hemimers” or “wingmers”.

[0201] [2-O-Me]--[2′-deoxy]--[2′-O-Me] Chimeric Phosphorothioate Oligonucleotides

[0202] Chimeric oligonucleotides having 2′-O-alkyl phosphorothioate and 2′-deoxy phosphorothioate oligonucleotide segments are synthesized using an Applied Biosystems automated DNA synthesizer Model 380B, as above. Oligonucleotides are synthesized using the automated synthesizer and 2′-deoxy-5′-dimethoxytrityl-3′-o-phosphoramidite for the DNA portion and 5′-dimethoxytrityl-2′-O-methyl-3′-O-phosphoramidite for 5′ and 3′ wings. The standard synthesis cycle is modified by increasing the wait step after the delivery of tetrazole and base to 600 s repeated four times for RNA and twice for 2′-O-methyl. The fully protected oligonucleotide is cleaved from the support and the phosphate group is deprotected in 3:1 ammonia/ethanol at room temperature overnight then lyophilized to dryness. Treatment in methanolic ammonia for 24 hrs at room temperature is then done to deprotect all bases and sample was again lyophilized to dryness. The pellet is resuspended in 1M TBAF in THF for 24 hrs at room temperature to deprotect the 2′ positions. The reaction is then quenched with 1M TEAA and the sample is then reduced to ½ volume by rotovac before being desalted on a G25 size exclusion column. The oligo recovered is then analyzed spectrophotometrically for yield and for purity by capillary electrophoresis and by mass spectrometry.

[0203] [2′-O-(2-Methoxyethyl)]--[2′-deoxy]--[2′-O-(Methoxyethyl)] Chimeric Phosphorothioate Oligonucleotides

[0204] [2′-O-(2-methoxyethyl)]--[2′-deoxy]--[-2′-O-(methoxy-ethyl)] chimeric phosphorothioate oligonucleotides were prepared as per the procedure above for the 2′-O-methyl chimeric oligonucleotide, with the substitution of 2′-O-(methoxyethyl) amidites for the 2′-O-methyl amidites.

[0205] [2′-O-(2-Methoxyethyl)Phosphodiester]--[2′-deoxy Phosphorothioate]--[2′-O-(2-Methoxyethyl) Phosphodiester] Chimeric Oligonucleotides

[0206] [2′-O-(2-methoxyethyl phosphodiester]--[2′-deoxy phosphorothioate]--[2′-O-(methoxyethyl) phosphodiester] chimeric oligonucleotides are prepared as per the above procedure for the 2′-O-methyl chimeric oligonucleotide with the substitution of 2′-O-(methoxyethyl) amidites for the 2′-O-methyl amidites, oxidization with iodine to generate the phosphodiester internucleotide linkages within the wing portions of the chimeric structures and sulfurization utilizing 3,H-1,2 benzodithiole-3-one 1,1 dioxide (Beaucage Reagent) to generate the phosphorothioate internucleotide linkages for the center gap.

[0207] Other chimeric oligonucleotides, chimeric oligonucleosides and mixed chimeric oligonucleotides/oligonucleosides are synthesized according to U.S. Pat. No. 5,623,065, herein incorporated by reference.

Example 6

[0208] Oligonucleotide Isolation

[0209] After cleavage from the controlled pore glass column (Applied Biosystems) and deblocking in concentrated ammonium hydroxide at 55° C. for 18 hours, the oligonucleotides or oligonucleosides are purified by precipitation twice out of 0.5 M NaCl with 2.5 volumes ethanol. Synthesized oligonucleotides were analyzed by polyacrylamide gel electrophoresis on denaturing gels and judged to be at least 85% full length material. The relative amounts of phosphorothioate and phosphodiester linkages obtained in synthesis were periodically checked by ³¹P nuclear magnetic resonance spectroscopy, and for some studies oligonucleotides were purified by HPLC, as described by Chiang et al., J. Biol. Chem. 1991, 266, 18162-18171. Results obtained with HPLC-purified material were similar to those obtained with non-HPLC purified material.

Example 7

[0210] Oligonucleotide Synthesis—96 Well Plate Format

[0211] Oligonucleotides were synthesized via solid phase P(III) phosphoramidite chemistry on an automated synthesizer capable of assembling 96 sequences simultaneously in a standard 96 well format. Phosphodiester internucleotide linkages were afforded by oxidation with aqueous iodine. Phosphorothioate internucleotide linkages were generated by sulfurization utilizing 3,H-1,2 benzodithiole-3-one 1,1 dioxide (Beaucage Reagent) in anhydrous acetonitrile. Standard base-protected beta-cyanoethyldiisopropyl phosphoramidites were purchased from commercial vendors (e.g. PE-Applied Biosystems, Foster City, Calif., or Pharmacia, Piscataway, N.J.). Non-standard nucleosides are synthesized as per known literature or patented methods. They are utilized as base protected beta-cyanoethyldiisopropyl phosphoramidites.

[0212] Oligonucleotides were cleaved from support and deprotected with concentrated NH₄OH at elevated temperature (55-60° C.) for 12-16 hours and the released product then dried in vacuo. The dried product was then re-suspended in sterile water to afford a master plate from which all analytical and test plate samples are then diluted utilizing robotic pipettors.

Example 8

[0213] Oligonucleotide Analysis—96 Well Plate Format

[0214] The concentration of oligonucleotide in each well was assessed by dilution of samples and UV absorption spectroscopy. The full-length integrity of the individual products was evaluated by capillary electrophoresis (CE) in either the 96 well format (Beckman P/ACE™ MDQ) or, for individually prepared samples, on a commercial CE apparatus (e.g., Beckman P/ACE™ 5000, ABI 270). Base and backbone composition was confirmed by mass analysis of the compounds utilizing electrospray-mass spectroscopy. All assay test plates were diluted from the master plate using single and multi-channel robotic pipettors. Plates were judged to be acceptable if at least 85% of the compounds on the plate were at least 85% full length.

Example 9

[0215] Cell Culture and Oligonucleotide Treatment

[0216] The effect of antisense compounds on target nucleic acid expression can be tested in any of a variety of cell types provided that the target nucleic acid is present at measurable levels. This can be routinely determined using, for example, PCR or Northern blot analysis. The following 7 cell types are provided for illustrative purposes, but other cell types can be routinely used, provided that the target is expressed in the cell type chosen. This can be readily determined by methods routine in the art, for example Northern blot analysis, Ribonuclease protection assays, or RT-PCR.

[0217] T-24 cells:

[0218] The human transitional cell bladder carcinoma cell line T-24 was obtained from the American Type Culture Collection (ATCC) (Manassas, Va.). T-24 cells were routinely cultured in complete McCoy's 5A basal media (Gibco/Life Technologies, Gaithersburg, Md.) supplemented with 10% fetal calf serum (Gibco/Life Technologies, Gaithersburg, Md.), penicillin 100 units per mL, and streptomycin 100 micrograms per mL (Gibco/Life Technologies, Gaithersburg, Md.). Cells were routinely passaged by trypsinization and dilution when they reached 90% confluence. Cells were seeded into 96-well plates (Falcon-Primaria #3872) at a density of 7000 cells/well for use in RT-PCR analysis.

[0219] For Northern blotting or other analysis, cells may be seeded onto 100 mm or other standard tissue culture plates and treated similarly, using appropriate volumes of medium and oligonucleotide.

[0220] A549 cells:

[0221] The human lung carcinoma cell line A549 was obtained from the American Type Culture Collection (ATCC) (Manassas, Va.). A549 cells were routinely cultured in DMEM basal media (Gibco/Life Technologies, Gaithersburg, Md.) supplemented with 10% fetal calf serum (Gibco/Life Technologies, Gaithersburg, Md.), penicillin 100 units per mL, and streptomycin 100 micrograms per mL (Gibco/Life Technologies, Gaithersburg, Md.). Cells were routinely passaged by trypsinization and dilution when they reached 90% confluence.

[0222] NHDF cells:

[0223] Human neonatal dermal fibroblast (NHDF) were obtained from the Clonetics Corporation (Walkersville Md.). NHDFs were routinely maintained in Fibroblast Growth Medium (Clonetics Corporation, Walkersville Md.) supplemented as recommended by the supplier. Cells were maintained for up to 10 passages as recommended by the supplier.

[0224] HEK cells:

[0225] Human embryonic keratinocytes (HEK) were obtained from the Clonetics Corporation (Walkersville Md.). HEKs were routinely maintained in Keratinocyte Growth Medium (Clonetics Corporation, Walkersville Md.) formulated as recommended by the supplier. Cells were routinely maintained for up to 10 passages as recommended by the supplier.

[0226] HepG2 cells:

[0227] The human hepatoblastoma cell line HepG2 was obtained from the American Type Culture Collection (Manassas, Va.). HepG2 cells were routinely cultured in Eagle's MEM supplemented with 10% fetal calf serum, non-essential amino acids, and 1 mM sodium pyruvate (Gibco/Life Technologies, Gaithersburg, Md.). Cells were routinely passaged by trypsinization and dilution when they reached 90% confluence. Cells were seeded into 96-well plates (Falcon-Primaria #3872) at a density of 7000 cells/well for use in RT-PCR analysis.

[0228] For Northern blotting or other analyses, cells may be seeded onto 100 mm or other standard tissue culture plates and treated similarly, using appropriate volumes of medium and oligonucleotide.

[0229] AML12 cells:

[0230] The AML12 (alpha mouse liver 12) cell line was established from hepatocytes from a mouse (CD1 strain, line MT42) transgenic for human TGF alpha. Cells are cultured in a 1:1 mixture of Dulbecco's modified Eagle's medium and Ham's F12 medium with 0.005 mg/ml insulin, 0.005 mg/ml transferrin, 5 ng/ml selenium, and 40 ng/ml dexamethasone, and 90%; 10% fetal bovine serum. For subculturing, spent medium is removed and fresh media of 0.25% trypsin, 0.03% EDTA solution is added. Fresh trypsin solution (1 to 2 ml) is added and the culture is left to sit at room temperature until the cells detach.

[0231] Cells were routinely passaged by trypsinization and dilution when they reached 90% confluence. Cells were seeded into 96-well plates (Falcon-Primaria #3872) at a density of 7000 cells/well for use in RT-PCR analysis.

[0232] For Northern blotting or other analyses, cells may be seeded onto 100 mm or other standard tissue culture plates and treated similarly, using appropriate volumes of medium and oligonucleotide.

[0233] Primary mouse hepatocytes:

[0234] Primary mouse hepatocytes were prepared from CD-1 mice purchased from Charles River Labs (Wilmington, Mass.) and were routinely cultured in Hepatoyte Attachment Media (Gibco) supplemented with 10% Fetal Bovine Serum (Gibco/Life Technologies, Gaithersburg, Md.), 250nM dexamethasone (Sigma), and 10 nM bovine insulin (Sigma). Cells were seeded into 96-well plates (Falcon-Primaria #3872) at a density of 10000 cells/well for use in RT-PCR analysis.

[0235] For Northern blotting or other analyses, cells are plated onto 100 mm or other standard tissue culture plates coated with rat tail collagen (200ug/mL) (Becton Dickinson) and treated similarly using appropriate volumes of medium and oligonucleotide.

[0236] Treatment with antisense compounds:

[0237] When cells reached 80% confluency, they were treated with oligonucleotide. For cells grown in 96-well plates, wells were washed once with 200 μL OPTI-MEM™-1 reduced-serum medium (Gibco BRL) and then treated with 130 μL of OPTI-MEM™-1 containing 3.75 μg/mL LIPOFECTIN™ (Gibco BRL) and the desired concentration of oligonucleotide. After 4-7 hours of treatment, the medium was replaced with fresh medium. Cells were harvested 16-24 hours after oligonucleotide treatment.

[0238] The concentration of oligonucleotide used varies from cell line to cell line. To determine the optimal oligonucleotide concentration for a particular cell line, the cells are treated with a positive control oligonucleotide at a range of concentrations. For human cells the positive control oligonucleotide is ISIS 13920, TCCGTCATCGCTCCTCAGGG, SEO ID NO: 1, a 2′-O-methoxyethyl gapmer (2′-O-methoxyethyls shown in bold) with a phosphorothioate backbone which is targeted to human H-ras. For mouse or rat cells the positive control oligonucleotide is ISIS 15770, ATGCATTCTGCCCCCAAGGA, SEO ID NO: 2, a 2′-O-methoxyethyl gapmer (2′-O-methoxyethyls shown in bold) with a phosphorothioate backbone which is targeted to both mouse and rat c-raf. The concentration of positive control oligonucleotide that results in 80% inhibition of c-Ha-ras (for ISIS 13920) or c-raf (for ISIS 15770) mRNA is then utilized as the screening concentration for new oligonucleotides in subsequent experiments for that cell line. If 80% inhibition is not achieved, the lowest concentration of positive control oligonucleotide that results in 60% inhibition of H-ras or c-raf mRNA is then utilized as the oligonucleotide screening concentration in subsequent experiments for that cell line. If 60% inhibition is not achieved, that particular cell line is deemed as unsuitable for oligonucleotide transfection experiments.

Example 10

[0239] Analysis of Oligonucleotide Inhibition of Microsomal Triglyceride Transfer Protein Expression

[0240] Antisense modulation of microsomal triglyceride transfer protein expression can be assayed in a variety of ways known in the art. For example, microsomal triglyceride transfer protein mRNA levels can be quantitated by, e.g., Northern blot analysis, competitive polymerase chain reaction (PCR), or real-time PCR (RT-PCR). Real-time quantitative PCR is presently preferred. RNA analysis can be performed on total cellular RNA or poly(A)+mRNA. Methods of RNA isolation are taught in, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 1, pp. 4.1.1-4.2.9 and 4.5.1-4.5.3, John Wiley & Sons, Inc., 1993. Northern blot analysis is routine in the art and is taught in, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 1, pp. 4.2.1-4.2.9, John Wiley & Sons, Inc., 1996. Real-time quantitative (PCR) can be conveniently accomplished using the commercially available ABI PRISM™ 7700 Sequence Detection System, available from PE-Applied Biosystems, Foster City, Calif. and used according to manufacturer's instructions.

[0241] Protein levels of microsomal triglyceride transfer protein can be quantitated in a variety of ways well known in the art, such as immunoprecipitation, Western blot analysis (immunoblotting), ELISA or fluorescence-activated cell sorting (FACS). Antibodies directed to microsomal triglyceride transfer protein can be identified and obtained from a variety of sources, such as the MSRS catalog of antibodies (Aerie Corporation, Birmingham, Mich.) , or can be prepared via conventional antibody generation methods. Methods for preparation of polyclonal antisera are taught in, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 2, pp. 11.12.1-11.12.9, John Wiley & Sons, Inc., 1997. Preparation of monoclonal antibodies is taught in, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 2, pp. 11.4.1-11.11.5, John Wiley & Sons, Inc., 1997.

[0242] Immunoprecipitation methods are standard in the art and can be found at, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 2, pp. 10.16.1-10.16.11, John Wiley & Sons, Inc., 1998. Western blot (immunoblot) analysis is standard in the art and can be found at, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 2, pp. 10.8.1-10.8.21, John Wiley & Sons, Inc., 1997. Enzyme-linked immunosorbent assays (ELISA) are standard in the art and can be found at, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 2, pp. 11.2.1-11.2.22, John Wiley & Sons, Inc., 1991.

Example 11

[0243] Poly(A)+mRNA isolation

[0244] Poly(A)+MRNA was isolated according to Miura et al., Clin. Chem., 1996, 42, 1758-1764. Other methods for poly(A)+MRNA isolation are taught in, for example, Ausubel, F. M. et al., Current Protocols in Molecular Biology, Volume 1, pp. 4.5.1-4.5.3, John Wiley & Sons, Inc., 1993. Briefly, for cells grown on 96-well plates, growth medium was removed from the cells and each well was washed with 200 μL cold PBS. 60 ULL lysis buffer (10 mM Tris-HCl, pH 7.6, 1 mM EDTA, 0.5 M NaCl, 0.5% NP-40, 20 mM vanadyl-ribonucleoside complex) was added to each well, the plate was gently agitated and then incubated at room temperature for five minutes. 55 μL of lysate was transferred to Oligo d(T) coated 96-well plates (AGCT Inc., Irvine Calif.). Plates were incubated for 60 minutes at room temperature, washed 3 times with 200 μL of wash buffer (10 mM Tris-HCl pH 7.6, 1 mM EDTA, 0.3 M NaCl). After the final wash, the plate was blotted on paper towels to remove excess wash buffer and then air-dried for 5 minutes. 60 μL of elution buffer (5 mM Tris-HCl pH 7.6), preheated to 70° C. was added to each well, the plate was incubated on a 90° C. hot plate for 5 minutes, and the eluate was then transferred to a fresh 96-well plate.

[0245] Cells grown on 100 mm or other standard plates may be treated similarly, using appropriate volumes of all solutions.

Example 12

[0246] Total RNA Isolation

[0247] Total RNA was isolated using an RNEASY 96™ kit and buffers purchased from Oiagen Inc. (Valencia Calif.) following the manufacturer's recommended procedures. Briefly, for cells grown on 96-well plates, growth medium was removed from the cells and each well was washed with 200 μL cold PBS. 100 μL Buffer RLT was added to each well and the plate vigorously agitated for 20 seconds. 100 μL of 70% ethanol was then added to each well and the contents mixed by pipetting three times up and down. The samples were then transferred to the RNEASY 96™ well plate attached to a QIAVAC™ manifold fitted with a waste collection tray and attached to a vacuum source. Vacuum was applied for 15 seconds. 1 mL of Buffer RW1 was added to each well of the RNEASY 96™ plate and the vacuum again applied for 15 seconds. 1 mL of Buffer RPE was then added to each well of the RNEASY 96™ plate and the vacuum applied for a period of 15 seconds. The Buffer RPE wash was then repeated and the vacuum was applied for an additional 10 minutes. The plate was then removed from the QIAVAC™ manifold and blotted dry on paper towels. The plate was then re-attached to the QIAVAC™ manifold fitted with a collection tube rack containing 1.2 mL collection tubes. RNA was then eluted by pipetting 60 μL water into each well, incubating 1 minute, and then applying the vacuum for 30 seconds. The elution step was repeated with an additional 60 μL water.

[0248] The repetitive pipetting and elution steps may be automated using a QIAGEN Bio-Robot 9604 (Qiagen, Inc., Valencia Calif.). Essentially, after lysing of the cells on the culture plate, the plate is transferred to the robot deck where the pipetting, DNase treatment and elution steps are carried out.

Example 13

[0249] Real-time Quantitative PCR Analysis of Microsomal Triglyceride Transfer Protein mRNA Levels

[0250] Quantitation of microsomal triglyceride transfer protein mRNA levels was determined by real-time quantitative PCR using the ABI PRISM™ 7700 Sequence Detection System (PE-Applied Biosystems, Foster City, Calif.) according to manufacturer's instructions. This is a closed-tube, non-gel-based, fluorescence detection system which allows high-throughput quantitation of polymerase chain reaction (PCR) products in real-time. As opposed to standard PCR, in which amplification products are quantitated after the PCR is completed, products in real-time quantitative PCR are quantitated as they accumulate. This is accomplished by including in the PCR reaction an oligonucleotide probe that anneals specifically between the forward and reverse PCR primers, and contains two fluorescent dyes. A reporter dye (e.g., JOE, FAM, or VIC, obtained from either Operon Technologies Inc., Alameda, Calif. or PE-Applied Biosystems, Foster City, Calif.) is attached to the 5′ end of the probe and a quencher dye (e.g., TAMPA, obtained from either Operon Technologies Inc., Alameda, Calif. or PE-Applied Biosystems, Foster City, Calif.) is attached to the 3′ end of the probe. When the probe and dyes are intact, reporter dye emission is quenched by the proximity of the 3′ quencher dye. During amplification, annealing of the probe to the target sequence creates a substrate that can be cleaved by the 5′-exonuclease activity of Taq polymerase. During the extension phase of the PCR amplification cycle, cleavage of the probe by Taq polymerase releases the reporter dye from the remainder of the probe (and hence from the quencher moiety) and a sequence-specific fluorescent signal is generated. With each cycle, additional reporter dye molecules are cleaved from their respective probes, and the fluorescence intensity is monitored at regular intervals by laser optics built into the ABI PRISM™ 7700 Sequence Detection System. In each assay, a series of parallel reactions containing serial dilutions of mRNA from untreated control samples generates a standard curve that is used to quantitate the percent inhibition after antisense oligonucleotide treatment of test samples.

[0251] Prior to quantitative PCR analysis, primer-probe sets specific to the target gene being measured are evaluated for their ability to be “multiplexed” with a GAPDH amplification reaction. In multiplexing, both the target gene and the internal standard gene GAPDH are amplified concurrently in a single sample. In this analysis, mRNA isolated from untreated cells is serially diluted. Each dilution is amplified in the presence of primer-probe sets specific for GAPDH only, target gene only (“single-plexing”), or both (multiplexing). Following PCR amplification, standard curves of GAPDH and target mRNA signal as a function of dilution are generated from both the single-plexed and multiplexed samples. If both the slope and correlation coefficient of the GAPDH and target signals generated from the multiplexed samples fall within 10% of their corresponding values generated from the single-plexed samples, the primer-probe set specific for that target is deemed multiplexable. Other methods of PCR are also known in the art.

[0252] PCR reagents were obtained from PE-Applied Biosystems, Foster City, Calif. RT-PCR reactions were carried out by adding 25 μL PCR cocktail (1×TAOMAN™ buffer A, 5.5 mM MgCl₂, 300 μM each of DATP, dCTP and dGTP, 600 μM of dUTP, 100 nM each of forward primer, reverse primer, and probe, 20 Units RNAse inhibitor, 1.25 Units AMPLITAQ GOLD™, and 12.5 Units MuLV reverse transcriptase) to 96 well plates containing 25 μL total RNA solution. The RT reaction was carried out by incubation for 30 minutes at 48° C. Following a 10 minute incubation at 95° C. to activate the AMPLITAQ GOLD™, 40 cycles of a two-step PCR protocol were carried out: 95° C. for 15 seconds (denaturation) followed by 60° C. for 1.5 minutes (annealing/extension).

[0253] Gene target quantities obtained by real time RT-PCR are normalized using either the expression level of GAPDH, a gene whose expression is constant, or by quantifying total RNA using RiboGreen™ (Molecular Probes, Inc. Eugene, Oreg.). GAPDH expression is quantified by real time RT-PCR, by being run simultaneously with the target, multiplexing, or separately. Total RNA is quantified using RiboGreen™ RNA quantification reagent from Molecular Probes. Methods of RNA quantification by RiboGreen™ are taught in Jones, L. J., et al, Analytical Biochemistry, 1998, 265, 368-374.

[0254] In this assay, 175 μL of RiboGreen™ working reagent (RiboGreenm reagent diluted 1:2865 in 10mM Tris-HCl, 1 mM EDTA, pH 7.5) is pipetted into a 96-well plate containing 25μL purified, cellular RNA. The plate is read in a CytoFluor 4000 (PE Applied Biosystems) with excitation at 480 nm and emission at 520 nm.

[0255] Probes and primers to human microsomal triglyceride transfer protein were designed to hybridize to a human microsomal triglyceride transfer protein sequence, using published sequence information (GenBank accession number NM_(—)000253, incorporated herein as SEQ ID NO: 3). For human microsomal triglyceride transfer protein the PCR primers were:

[0256] forward primer: CGTGGGCTACCGCATTTC (SEQ ID NO: 4)

[0257] reverse primer: TCATCATCACCATCAGGATTCC (SEQ ID NO: 5) and the

[0258] PCR probe was: FAM-TCCAACGTGGATGTGGCCTTACTATGG-TAMRA (SEQ ID NO: 6) where FAM (PE-Applied Biosystems, Foster City, Calif.) is the fluorescent reporter dye) and TAMRA (PE-Applied Biosystems, Foster City, Calif.) is the quencher dye. For human GAPDH the PCR primers were:

[0259] forward primer: GAAGGTGAAGGTCGGAGTC (SEQ ID NO: 7)

[0260] reverse primer: GAAGATGGTGATGGGATTTC (SEQ ID NO: 8) and the

[0261] PCR probe was: 5′ JOE-CAAGCTTCCCGTTCTCAGCC-TAMRA 3′ (SEQ ID NO: 9) where JOE (PE-Applied Biosystems, Foster City, Calif.) is the fluorescent reporter dye) and TAMRA (PE-Applied Biosystems, Foster City, Calif.) is the quencher dye.

[0262] Probes and primers to mouse microsomal triglyceride transfer protein were designed to hybridize to a mouse microsomal triglyceride transfer protein sequence, using published sequence information (GenBank accession number NM_(—)008642, incorporated herein as SEQ ID NO: 10). For mouse microsomal triglyceride transfer protein the PCR primers were:

[0263] forward primer: GAGCGGTCTGGATTTACA (SEQ ID NO: 11)

[0264] reverse primer: AGGTAGTGACAGATGTGGCTTTTG (SEQ ID NO: 12) and the PCR probe was: FAM-CAAACCAGGTGCTGGGCGTCAGT-TAMRA (SEQ ID NO: 13) where FAM (PE-Applied Biosystems, Foster City, Calif.) is the fluorescent reporter dye) and TAMRA (PE-Applied Biosystems, Foster City, Calif.) is the quencher dye. For mouse GAPDH the PCR primers were: forward primer: GGCAAATTCAACGGCACAGT (SEQ ID NO: 14) reverse primer: GGGTCTCGCTCCTGGAAGAT (SEQ ID NO:15) and the PCR probe was: 5′ JOE-AAGGCCGAGAATGGGAAGCTTGTCATC-TAMPA 3′ (SEQ ID NO: 16) where JOE (PE-Applied Biosystems, Foster City, Calif.) is the fluorescent reporter dye) and TAMRA (PE-Applied Biosystems, Foster City, Calif.) is the quencher dye.

Example 14

[0265] Northern Blot Analysis of Microsomal Triglyceride Transfer Protein mRNA Levels

[0266] Eighteen hours after antisense treatment, cell monolayers were washed twice with cold PBS and lysed in 1 mL RNAZOL™ (TEL-TEST “B” Inc., Friendswood, Tex.). Total RNA was prepared following manufacturer's recommended protocols. Twenty micrograms of total RNA was fractionated by electrophoresis through 1.2% agarose gels containing 1.1% formaldehyde using a MOPS buffer system (AMRESCO, Inc. Solon, OH). RNA was transferred from the gel to HYBOND™-N+ nylon membranes (Amersham Pharmacia Biotech, Piscataway, N.J.) by overnight capillary transfer using a Northern/Southern Transfer buffer system (TEL-TEST “B” Inc., Friendswood, Tex.). RNA transfer was confirmed by UV visualization. Membranes were fixed by UV cross-linking using a STRATALINKER™ UV Crosslinker 2400 (Stratagene, Inc, La Jolla, Calif.) and then robed using QUICKHYB™ hybridization solution (Stratagene, La Jolla, Calif.) using manufacturer's recommendations for stringent conditions.

[0267] To detect human microsomal triglyceride transfer protein, a human microsomal triglyceride transfer protein specific probe was prepared by PCR using the forward primer CGTGGGCTACCGCATTTC (SEQ ID NO: 4) and the reverse primer TCATCATCACCATCAGGATTCC (SEQ ID NO: 5). To normalize for variations in loading and transfer efficiency membranes were stripped and probed for human glyceraldehyde-3-phosphate dehydrogenase (GAPDH) RNA (Clontech, Palo Alto, Calif.).

[0268] To detect mouse microsomal triglyceride transfer protein, a human microsomal triglyceride transfer protein specific probe was prepared by PCR using the forward primer GAGCGGTCTGGATTTACA (SEQ ID NO: 11) and the reverse primer AGGTAGTGACAGATGTGGCTTTTG (SEQ ID NO: 12). To normalize for variations in loading and transfer efficiency membranes were stripped and probed for mouse glyceraldehyde-3-phosphate dehydrogenase (GAPDH) RNA (Clontech, Palo Alto, Calif.).

[0269] Hybridized membranes were visualized and quantitated using a PHOSPHORIMAGER™ and IMAGEQUANT™ Software V3.3 (Molecular Dynamics, Sunnyvale, Calif.). Data was normalized to GAPDH levels in untreated controls.

Example 15

[0270] Antisense Inhibition of Human Microsomal Triglyceride Transfer Protein Expression by Chimeric Phosphorothioate Oligonucleotides Having 2′-MOE wings and a Deoxy Gap

[0271] In accordance with the present invention, a series of oligonucleotides were designed to target different regions of the human microsomal triglyceride transfer protein RNA, using published sequence (GenBank accession number NM_(—)000253, incorporated herein as SEQ ID NO: 3). The oligonucleotides are shown in Table 1. “Target site” indicates the first (5′-most) nucleotide number on the particular target sequence to which the oligonucleotide binds. All compounds in Table 1 are chimeric oligonucleotides (“gapmers”) 20 nucleotides in length, composed of a central “gap” region consisting of ten 2′-deoxynucleotides, which is flanked on both sides (5′ and 3′-directions) by five-nucleotide “wings”. The wings are composed of 2′-methoxyethyl (2′-MOE) nucleotides. The internucleoside (backbone) linkages are phosphorothioate (P═S) throughout the oligonucleotide. All cytidine residues are 5-methylcytidines. The compounds were analyzed for their effect on human microsomal triglyceride transfer protein mRNA levels in AML12 cells by quantitative real-time PCR as described in other examples herein. Data are averages from two experiments. If present, “N.D.” indicates “no data”. TABLE 1 Inhibition of human microsomal triglyceride transfer protein mBNA levels by chimeric phosphorothioate oligonucleotides having 2′-MOE wings and a deoxy gap TARGET TARGET SEQ ID ISIS # REGION SEQ ID NO SITE SEQUENCE % INBIB NO 144407 5′UTR 3 41 CAGTGCCCAGCTAGGAGTCA 36 17 144408 5′UTR 3 52 TCAACTGCATCCAGTGCCCA 30 18 144409 Start Codon 3 71 TCATATTGACCAGCAATCCT 31 19 144410 Coding 3 141 CCAGTTGTGTGACCTTTAAC 38 20 144411 Coding 3 179 ACGTGAGCTTGTACAGCCGG 28 21 144412 Coding 3 241 GCGGTAGCCCACGCTGTCTT 34 22 144413 Coding 3 281 GATTCCTCCATAGTAAGGCC 91 23 144414 Coding 3 451 GATTAGATGAAGGAGCGTAG 0 24 144415 Coding 3 561 GTGGTTCCAGAGCTTAACTG 0 25 144416 Coding 3 725 AGGTGGTGACAGATGTAGCT 27 26 144417 Coding 3 891 GCTGCAGCCTGCTTTCCAGA 9 27 144418 Coding 3 961 ACAGTGGCTCTGGAAGACCT 0 28 144419 Coding 3 1001 TGGTGGACCGCCAGAGCTCC 0 29 144420 Coding 3 1161 GAGGTGACAGCATCCACCAG 21 30 144421 Coding 3 1191 ATGGCTTCTAATGAGTCTGA 13 31 144422 Coding 3 1238 CCTGGAGGATAATGCTGCTG 37 32 144423 Coding 3 1371 AGTGTCCCAGTGATGATCAT 41 33 144424 Coding 3 1491 AGCAGATACATCCTGGTGTC 23 34 144425 Coding 3 1561 CCCTTCTCCTGCTTCTGCAT 22 35 144426 Coding 3 1589 GAGCAGTGGTAGCCAGGTGG 22 36 144427 Coding 3 1639 TAAGGTCTTCTTCACCTCAT 8 37 144428 Coding 3 1701 GCAGCTGCAGCAGTGCGCAC 19 38 144429 Coding 3 1741 CTTGACGTCCATGTAGGATG 0 39 144430 Coding 3 1931 CTATGTAGCCAGTGTAGGCA 0 40 144431 Coding 3 1981 CGAGTAGAGAATGTCTAGGC 26 41 144432 Coding 3 2051 TACCGTGAAGACCAGCCTTC 0 42 144433 Coding 3 2091 ATTAAGGCTTCCAGTCCTTG 0 43 144434 Coding 3 2331 CCCTGGACCTCTATATTGGC 0 44 144435 Coding 3 2381 GATACCACAAGCTAAACTCC 0 45 144436 Coding 3 2451 GAGGAGTCCACTGTGATGTC 29 46 144437 Coding 3 2481 GTACTGGTTTCCAGGCCAGC 32 47 144438 Coding 3 2571 GCTTCATCCTTGTCCATCTG 53 48 144439 Coding 3 2741 CGCTGGAAGTACTATCCGGC 52 49 144440 Stop Codon 3 2769 AATATCACAGGTCAGTTTCA 40 50 144441 3′UTR 3 2811 CATGCCACATTGTGTCCCTT 60 51 144442 3′UTR 3 2841 CGCTGTGCTCTCAGAGAGCA 57 52 144443 3′UTR 3 2928 GTAGCATACTGCATATACCC 51 53 144444 3′UTR 3 2951 GATGATTCAAAATGACGCTG 32 54 144445 3′UTR 3 3001 GATTTGAGAGAGGTATAAGT 18 55 144446 3′UTR 3 3031 GAGAATAACTATTCTGACTG 28 56 144447 3′UTR 3 3133 GAGCTTCATATACATTGATC 70 57 144448 3′UTR 3 3161 CCCGTCATGCTTAAGGAAGT 49 58 144449 3′UTR 3 3361 ATGTGCCTTCTACCTTAAGG 35 59

[0272] As shown in Table 1, SEQ ID NOs 17, 18, 19, 20, 22, 23, 32, 33, 47, 48, 49, 50, 51, 52, 53, 54, 57, 58 and 59 demonstrated at least 30% inhibition of human microsomal triglyceride transfer protein expression in this assay and are therefore preferred. The target sites to which these preferred sequences are complementary are herein referred to as “active sites” and are therefore preferred sites for targeting by compounds of the present invention.

Example 16

[0273] Antisense Inhibition of Mouse Microsomal Triglyceride Transfer Protein Expression by Chimeric Phosphorothioate Oligonucleotides Having 2′-MOE Wings and a Deoxy Gap

[0274] In accordance with the present invention, a series of oligonucleotides were designed to target different regions of the mouse microsomal triglyceride transfer protein RNA, using published sequence (GenBank accession number NM_(—)008642, incorporated herein as SEQ ID NO: 10). The oligonucleotides are shown in Table 2. “Target site” indicates the first (5′-most) nucleotide number on the particular target sequence to which the oligonucleotide binds. All compounds in Table 2 are chimeric oligonucleotides (“gapmers”) 20 nucleotides in length, composed of a central “gap” region consisting of ten 2′-deoxynucleotides, which is flanked on both sides (5′ and 3′ directions) by five-nucleotide “wings”. The wings are composed of 2′-methoxyethyl (2′-MOE)_(n)ucleotides. The internucleoside (backbone) linkages are phosphorothioate (P═S) throughout the oligonucleotide. All cytidine residues are 5-methylcytidines. The compounds were analyzed for their effect on mouse microsomal triglyceride transfer protein mRNA levels in primary hepatocytes by quantitative real-time PCR as described in other examples herein. Data are averages from two experiments. If present, “N.D.” indicates “no data”. TABLE 2 Inhibition of mouse microsomal triglyceride transfer protein mRNA levels by chimeric phosphorothioate oligonucleotides having 2′ -MOE wings and a deoxy gap TARGET TARGET SEQ ID ISIS # REGION SEQ ID NO SITE SEQUENCE % INBIB NO 144467 5′UTR 10 1 GCTCCCTCTGCCACATCCAG 0 60 144468 Start Codon 10 11 GATCATGCTGGCTCCCTCTG 0 61 144469 Coding 10 121 GAGTACGTGAGCTTGTATAG 0 62 144470 Coding 10 176 GTAGCCCACGCTGTCTTGCG 5 63 144471 Coding 10 231 CATCACCATCAGGATTCCTC 21 64 144472 Coding 10 317 GCCCTGGAAGATGCTCTTCT 0 65 144473 Coding 10 358 GCCTCCAGGTTGTCCTTCCC 1 66 144474 Coding 10 412 TAGAACTCCTTGACCTTCCC 16 67 144475 Coding 10 475 TGGAATAAGCTAGCCAAGCC 18 68 144476 Coding 10 521 CCCAGAGATATCTACCTCGT 19 69 144477 Coding 10 631 CCCAGCACCTGGTTTGCCGT 94 70 144478 Coding 10 714 CCCTGGTCTCTTCTGCAAGC 41 71 144479 Coding 10 831 CACCTGCCACTTGCTTCCCG 65 72 144480 Coding 10 891 GCTCGAGGACCTGTCCCACA 51 73 144481 Coding 10 931 TTCCAGTGCTCCGCCAGAGA 33 74 144482 Coding 10 1021 GAAGTCCGGAGGTGCTGGAT 3 75 144483 Coding 10 1101 CAGAGGTGACGGCATCCACC 22 76 144484 Coding 10 1176 CCTGGAGTATGATACTGCTG 48 77 144485 Coding 10 1281 CTCTGATGTCGTTGCTTGCA 50 78 144486 Coding 10 1331 ATTCTGACACAGCTTCCTGA 34 79 144487 Coding 10 1381 CCCAGGATCAGCTTCTTAGC 19 80 144488 Coding 10 1491 CAGCCTCAGCATACTTCAGA 35 81 144489 Coding 10 1511 GTGGCTGACGGGCCCTTCTC 42 82 144490 Coding 10 1601 ACGATTCTGGTGGTATATCC 23 83 144491 Coding 10 1641 CAGCAGCGGCAGTTGTGCGC 26 84 144492 Coding 10 1741 TGCACAACGGTGAGCATGTA 39 85 144493 Coding 10 1859 GCCAGTATAGGCAGAAGAGG 24 86 144494 Coding 10 1901 AAGGCTGTATGTGGACGCTG 27 87 144495 Coding 10 1931 CAGAATGCCAGAGCCAGAGT 42 88 144496 Coding 10 2031 CTGCAATTAAGCCTTCCAGC 40 89 144497 Coding 10 2051 CTCTCCTTCATCAGGAGTGG 57 90 144498 Coding 10 2081 TGACATGCCAGCATAAGAGT 44 91 144499 Coding 10 2181 CGCTGACAGGGTCGCCGGAT 38 92 144500 Coding 10 2192 CCCTTTCACCACGCTGACAG 34 93 144501 Coding 10 2271 GACCACCCTGGATCTCCATA 52 94 144502 Coding 10 2321 CTCGCGATACCACAGACTGA 51 95 144503 Coding 10 2362 GTTATCACCACAGCCACCCG 50 96 144504 Coding 10 2441 GAACTCCAGCCCAGCCTCTG 0 97 144505 Coding 10 2501 AGCCTTGTCCATCTGCATGC 24 98 144506 Coding 10 2601 CACATCCGGCCACTAGGCTC 0 99 144507 Coding 10 2631 TCTCAGAGTTCTGTTGATGG 0 100 144508 3′UTR 10 2731 CGTCATAGCATATCGTTCTG 0 101 144509 3′UTR 10 2761 ACTGTGCTCTCAGAGAGCAA 0 102 144510 3′UTR 10 2849 GGTCTTCTCCTGAATAGGTT 0 103 158657 Coding 10 81 GGCCAGTTGTGTGACCTTTA N.D. 104 158658 Coding 10 141 CATCAAGAAACACTTCAGTG N.D. 105 158659 Coding 10 201 CAACGTCCACATCAGATGAG N.D. 106 158660 Coding 10 261 CTGTTATCGTGACTTGGATC N.D. 107 158661 Coding 10 381 GAAGAAGCATGGGTCTCTGC N.D. 108 158662 Coding 10 441 CTATGCCCACTGGCTCGTTT N.D. 109 158663 Coding 10 501 TGGTAGTTCCAGAGCTTAGC N.D. 110 158664 Coding 10 541 TGGTAGGTCACTTTACAATC N.D. 111 158665 Coding 10 651 ATGTGGCTTTTGAACTGACG N.D. 112 158666 Coding 10 671 TATCTTGTAGGTAGTGACAG N.D. 113 158667 Coding 10 691 GCGGTGACAAAGCTGTCCTC N.D. 114 158668 Coding 10 910 GGGCATCCTTTGCAGACACG N.D. 115 158669 Coding 10 981 CAGCCTCGGCCTTGGACAGG N.D. 116 158670 Coding 10 1001 GAAGGCCAGGAAGCTCTGGA N.D. 117 158671 Coding 10 1121 TAGCGAGTCTGGAGTCTGAG N.D. 118 158672 Coding 10 1301 AATGATGATCATAACCGACT N.D. 119 158673 Coding 10 1351 GCCTTGAGCTTGCAGCCTTC N.D. 120 158674 Coding 10 1431 CCAGCAGGTACATTGTGGTG N.D. 121 158675 Coding 10 1551 TGAAGGAGACATCGTATCTC N.D. 122 158676 Coding 10 1621 ACCGTCTTCTCATGAACCTT N.D. 123 158677 Coding 10 1681 ATGTTCTTCACATCCATGTA N.D. 124 158678 Coding 10 1801 ATCTCCTTGAGAACTCGACG N.D. 125 158679 Coding 10 1821 GGTCATAATTGTGAACAGCC N.D. 126 158680 Coding 10 2001 CAATCACCACCTGACTACCA N.D. 127 158681 Coding 10 2101 TGAACATCAAACAGGATGGC N.D. 128 158682 Coding 10 2211 GGTCTATTAACAGAATAAGC N.D. 129 158683 Coding 10 2231 CAGCTGAATATCCTGAGAAT N.D. 130 158684 Coding 10 2331 GGGTTTTAGACTCGCGATAC N.D. 131 158685 Coding 10 2381 ATCCACTGTGACGTCGCTGG N.D. 132 158686 Coding 10 2461 GAGAACTGCACTGTGGAGAT N.D. 133 158687 Coding 10 2554 CTGCCTGTAGATAGCCTTTC N.D. 134 158688 Coding 10 2651 TGGGAATACCACGTTGCACA N.D. 135 158689 3′UTR 10 2781 ATACAGGTAAATATGTAAAC N.D. 136 158690 3′UTR 10 2821 ATCAACTGAAGTTCTCCACT N.D. 137

[0275] As shown in Table 2, SEQ ID Nos 70, 71, 72, 73, 74, 77, 78, 79, 81, 82, 85, 88, 89, 91, 92, 93, 94, 95 and 96 demonstrated at least 30% inhibition of mouse microsomal triglyceride transfer protein expression in this assay and are therefore preferred. The target sites to which these preferred sequences are complementary are herein referred to as “active sites” and are therefore preferred sites for targeting by compounds of the present invention.

Example 17

[0276] Western Blot Analysis of Microsomal Triglyceride Transfer Protein Levels

[0277] Western blot analysis (immunoblot analysis) is carried out using standard methods. Cells are harvested 16-20 h after oligonucleotide treatment, washed once with PBS, suspended in Laemmli buffer (100 ul/well), boiled for 5 minutes and loaded on a 16% SDS-PAGE gel. Gels are run for 1.5 hours at 150 V, and transferred to membrane for western blotting. Appropriate primary antibody directed to microsomal triglyceride transfer protein is used, with a radiolabelled or fluorescently labeled secondary antibody directed against the primary antibody species. Bands are visualized using a PHOSPHORIMAGER™ (Molecular Dynamics, Sunnyvale Calif.).

1 137 1 20 DNA Artificial Sequence Antisense Oligonucleotide 1 tccgtcatcg ctcctcaggg 20 2 20 DNA Artificial Sequence Antisense Oligonucleotide 2 atgcattctg cccccaagga 20 3 3392 DNA Homo sapiens CDS (87)...(2771) 3 actccctcac tggctgccat tgaaagagtc cacttctcag tgactcctag ctgggcactg 60 gatgcagttg aggattgctg gtcaat atg att ctt ctt gct gtg ctt ttt ctc 113 Met Ile Leu Leu Ala Val Leu Phe Leu 1 5 tgc ttc att tcc tca tat tca gct tct gtt aaa ggt cac aca act ggt 161 Cys Phe Ile Ser Ser Tyr Ser Ala Ser Val Lys Gly His Thr Thr Gly 10 15 20 25 ctc tca tta aat aat gac cgg ctg tac aag ctc acg tac tcc act gaa 209 Leu Ser Leu Asn Asn Asp Arg Leu Tyr Lys Leu Thr Tyr Ser Thr Glu 30 35 40 gtt ctt ctt gat cgg ggc aaa gga aaa ctg caa gac agc gtg ggc tac 257 Val Leu Leu Asp Arg Gly Lys Gly Lys Leu Gln Asp Ser Val Gly Tyr 45 50 55 cgc att tcc tcc aac gtg gat gtg gcc tta cta tgg agg aat cct gat 305 Arg Ile Ser Ser Asn Val Asp Val Ala Leu Leu Trp Arg Asn Pro Asp 60 65 70 ggt gat gat gac cag ttg atc caa ata acg atg aag gat gta aat gtt 353 Gly Asp Asp Asp Gln Leu Ile Gln Ile Thr Met Lys Asp Val Asn Val 75 80 85 gaa aat gtg aat cag cag aga gga gag aag agc atc ttc aaa gga aaa 401 Glu Asn Val Asn Gln Gln Arg Gly Glu Lys Ser Ile Phe Lys Gly Lys 90 95 100 105 agc cca tct aaa ata atg gga aag gaa aac ttg gaa gct ctg caa aga 449 Ser Pro Ser Lys Ile Met Gly Lys Glu Asn Leu Glu Ala Leu Gln Arg 110 115 120 cct acg ctc ctt cat cta atc cat gga aag gtc aaa gag ttc tac tca 497 Pro Thr Leu Leu His Leu Ile His Gly Lys Val Lys Glu Phe Tyr Ser 125 130 135 tat caa aat gag gca gtg gcc ata gaa aat atc aag aga ggt ctg gct 545 Tyr Gln Asn Glu Ala Val Ala Ile Glu Asn Ile Lys Arg Gly Leu Ala 140 145 150 agc cta ttt cag aca cag tta agc tct gga acc acc aat gag gta gat 593 Ser Leu Phe Gln Thr Gln Leu Ser Ser Gly Thr Thr Asn Glu Val Asp 155 160 165 atc tct gga aat tgt aaa gtg acc tac cag gct cat caa gac aaa gtg 641 Ile Ser Gly Asn Cys Lys Val Thr Tyr Gln Ala His Gln Asp Lys Val 170 175 180 185 atc aaa att aag gcc ttg gat tca tgc aaa ata gcg agg tct gga ttt 689 Ile Lys Ile Lys Ala Leu Asp Ser Cys Lys Ile Ala Arg Ser Gly Phe 190 195 200 acg acc cca aat cag gtc ttg ggt gtc agt tca aaa gct aca tct gtc 737 Thr Thr Pro Asn Gln Val Leu Gly Val Ser Ser Lys Ala Thr Ser Val 205 210 215 acc acc tat aag ata gaa gac agc ttt gtt ata gct gtg ctt gct gaa 785 Thr Thr Tyr Lys Ile Glu Asp Ser Phe Val Ile Ala Val Leu Ala Glu 220 225 230 gaa aca cac aat ttt gga ctg aat ttc cta caa acc att aag ggg aaa 833 Glu Thr His Asn Phe Gly Leu Asn Phe Leu Gln Thr Ile Lys Gly Lys 235 240 245 ata gta tcg aag cag aaa tta gag ctg aag aca acc gaa gca ggc cca 881 Ile Val Ser Lys Gln Lys Leu Glu Leu Lys Thr Thr Glu Ala Gly Pro 250 255 260 265 aga ttg atg tct gga aag cag gct gca gcc ata atc aaa gca gtt gat 929 Arg Leu Met Ser Gly Lys Gln Ala Ala Ala Ile Ile Lys Ala Val Asp 270 275 280 tca aag tac acg gcc att ccc att gtg ggg cag gtc ttc cag agc cac 977 Ser Lys Tyr Thr Ala Ile Pro Ile Val Gly Gln Val Phe Gln Ser His 285 290 295 tgt aaa gga tgt cct tct ctc tcg gag ctc tgg cgg tcc acc agg aaa 1025 Cys Lys Gly Cys Pro Ser Leu Ser Glu Leu Trp Arg Ser Thr Arg Lys 300 305 310 tac ctg cag cct gac aac ctt tcc aag gct gag gct gtc aga aac ttc 1073 Tyr Leu Gln Pro Asp Asn Leu Ser Lys Ala Glu Ala Val Arg Asn Phe 315 320 325 ctg gcc ttc att cag cac ctc agg act gcg aag aaa gaa gag atc ctt 1121 Leu Ala Phe Ile Gln His Leu Arg Thr Ala Lys Lys Glu Glu Ile Leu 330 335 340 345 caa ata cta aag atg gaa aat aag gaa gta tta cct cag ctg gtg gat 1169 Gln Ile Leu Lys Met Glu Asn Lys Glu Val Leu Pro Gln Leu Val Asp 350 355 360 gct gtc acc tct gct cag acc tca gac tca tta gaa gcc att ttg gac 1217 Ala Val Thr Ser Ala Gln Thr Ser Asp Ser Leu Glu Ala Ile Leu Asp 365 370 375 ttt ttg gat ttc aaa agt gac agc agc att atc ctc cag gag agg ttt 1265 Phe Leu Asp Phe Lys Ser Asp Ser Ser Ile Ile Leu Gln Glu Arg Phe 380 385 390 ctc tat gcc tgt gga ttt gct tct cat ccc aat gaa gaa ctc ctg aga 1313 Leu Tyr Ala Cys Gly Phe Ala Ser His Pro Asn Glu Glu Leu Leu Arg 395 400 405 gcc ctc att agt aag ttc aaa ggt tct att ggt agc agt gac atc aga 1361 Ala Leu Ile Ser Lys Phe Lys Gly Ser Ile Gly Ser Ser Asp Ile Arg 410 415 420 425 gaa act gtt atg atc atc act ggg aca ctt gtc aga aag ttg tgt cag 1409 Glu Thr Val Met Ile Ile Thr Gly Thr Leu Val Arg Lys Leu Cys Gln 430 435 440 aat gaa ggc tgc aaa ctc aaa gca gta gtg gaa gct aag aag tta atc 1457 Asn Glu Gly Cys Lys Leu Lys Ala Val Val Glu Ala Lys Lys Leu Ile 445 450 455 ctg gga gga ctt gaa aaa gca gag aaa aaa gag gac acc agg atg tat 1505 Leu Gly Gly Leu Glu Lys Ala Glu Lys Lys Glu Asp Thr Arg Met Tyr 460 465 470 ctg ctg gct ttg aag aat gcc ctg ctt cca gaa ggc atc cca agt ctt 1553 Leu Leu Ala Leu Lys Asn Ala Leu Leu Pro Glu Gly Ile Pro Ser Leu 475 480 485 ctg aag tat gca gaa gca gga gaa ggg ccc atc agc cac ctg gct acc 1601 Leu Lys Tyr Ala Glu Ala Gly Glu Gly Pro Ile Ser His Leu Ala Thr 490 495 500 505 act gct ctc cag aga tat gat ctc cct ttc ata act gat gag gtg aag 1649 Thr Ala Leu Gln Arg Tyr Asp Leu Pro Phe Ile Thr Asp Glu Val Lys 510 515 520 aag acc tta aac aga ata tac cac caa aac cgt aaa gtt cat gaa aag 1697 Lys Thr Leu Asn Arg Ile Tyr His Gln Asn Arg Lys Val His Glu Lys 525 530 535 act gtg cgc act gct gca gct gct atc att tta aat aac aat cca tcc 1745 Thr Val Arg Thr Ala Ala Ala Ala Ile Ile Leu Asn Asn Asn Pro Ser 540 545 550 tac atg gac gtc aag aac atc ctg ctg tct att ggg gag ctt ccc caa 1793 Tyr Met Asp Val Lys Asn Ile Leu Leu Ser Ile Gly Glu Leu Pro Gln 555 560 565 gaa atg aat aaa tac atg ctc gcc att gtt caa gac atc cta cgt ttg 1841 Glu Met Asn Lys Tyr Met Leu Ala Ile Val Gln Asp Ile Leu Arg Leu 570 575 580 585 gaa atg cct gca agc aaa att gtc cgt cga gtt ctg aag gaa atg gtc 1889 Glu Met Pro Ala Ser Lys Ile Val Arg Arg Val Leu Lys Glu Met Val 590 595 600 gct cac aat tat gac cgt ttc tcc agg agt gga tct tct tct gcc tac 1937 Ala His Asn Tyr Asp Arg Phe Ser Arg Ser Gly Ser Ser Ser Ala Tyr 605 610 615 act ggc tac ata gaa cgt agt ccc cgt tcg gca tct act tac agc cta 1985 Thr Gly Tyr Ile Glu Arg Ser Pro Arg Ser Ala Ser Thr Tyr Ser Leu 620 625 630 gac att ctc tac tcg ggt tct ggc att cta agg aga agt aac ctg aac 2033 Asp Ile Leu Tyr Ser Gly Ser Gly Ile Leu Arg Arg Ser Asn Leu Asn 635 640 645 atc ttt cag tac att ggg aag gct ggt ctt cac ggt agc cag gtg gtt 2081 Ile Phe Gln Tyr Ile Gly Lys Ala Gly Leu His Gly Ser Gln Val Val 650 655 660 665 att gaa gcc caa gga ctg gaa gcc tta atc gca gcc acc cct gac gag 2129 Ile Glu Ala Gln Gly Leu Glu Ala Leu Ile Ala Ala Thr Pro Asp Glu 670 675 680 ggg gag gag aac ctt gac tcc tat gct ggt atg tca gcc atc ctc ttt 2177 Gly Glu Glu Asn Leu Asp Ser Tyr Ala Gly Met Ser Ala Ile Leu Phe 685 690 695 gat gtt cag ctc aga cct gtc acc ttt ttc aac gga tac agt gat ttg 2225 Asp Val Gln Leu Arg Pro Val Thr Phe Phe Asn Gly Tyr Ser Asp Leu 700 705 710 atg tcc aaa atg ctg tca gca tct ggc gac cct atc agt gtg gtg aaa 2273 Met Ser Lys Met Leu Ser Ala Ser Gly Asp Pro Ile Ser Val Val Lys 715 720 725 gga ctt att ctg cta ata gat cat tct cag gaa ctt cag tta caa tct 2321 Gly Leu Ile Leu Leu Ile Asp His Ser Gln Glu Leu Gln Leu Gln Ser 730 735 740 745 gga cta aaa gcc aat ata gag gtc cag ggt ggt cta gct att gat att 2369 Gly Leu Lys Ala Asn Ile Glu Val Gln Gly Gly Leu Ala Ile Asp Ile 750 755 760 tca ggt gca atg gag ttt agc ttg tgg tat cgt gag tct aaa acc cga 2417 Ser Gly Ala Met Glu Phe Ser Leu Trp Tyr Arg Glu Ser Lys Thr Arg 765 770 775 gtg aaa aat agg gtg act gtg gta ata acc act gac atc aca gtg gac 2465 Val Lys Asn Arg Val Thr Val Val Ile Thr Thr Asp Ile Thr Val Asp 780 785 790 tcc tct ttt gtg aaa gct ggc ctg gaa acc agt aca gaa aca gaa gca 2513 Ser Ser Phe Val Lys Ala Gly Leu Glu Thr Ser Thr Glu Thr Glu Ala 795 800 805 ggc ttg gag ttt atc tcc aca gtg cag ttt tct cag tac cca ttc tta 2561 Gly Leu Glu Phe Ile Ser Thr Val Gln Phe Ser Gln Tyr Pro Phe Leu 810 815 820 825 gtt tgc atg cag atg gac aag gat gaa gct cca ttc agg caa ttt gag 2609 Val Cys Met Gln Met Asp Lys Asp Glu Ala Pro Phe Arg Gln Phe Glu 830 835 840 aaa aag tac gaa agg ctg tcc aca ggc aga ggt tat gtc tct cag aaa 2657 Lys Lys Tyr Glu Arg Leu Ser Thr Gly Arg Gly Tyr Val Ser Gln Lys 845 850 855 aga aaa gaa agc gta tta gca gga tgt gaa ttc ccg ctc cat caa gag 2705 Arg Lys Glu Ser Val Leu Ala Gly Cys Glu Phe Pro Leu His Gln Glu 860 865 870 aac tca gag atg tgc aaa gtg gtg ttt gcc cct cag ccg gat agt act 2753 Asn Ser Glu Met Cys Lys Val Val Phe Ala Pro Gln Pro Asp Ser Thr 875 880 885 tcc agc gga tgg ttt tga aactgacctg tgatatttta cttgaatttg 2801 Ser Ser Gly Trp Phe 890 tctccccgaa agggacacaa tgtggcatga ctaagtactt gctctctgag agcacagcgt 2861 ttacatattt acctgtattt aagatttttg taaaaagcta caaaaaactg cagtttgatc 2921 aaatttgggt atatgcagta tgctacccac agcgtcattt tgaatcatca tgtgacgctt 2981 tcaacaacgt tcttagttta cttatacctc tctcaaatct catttggtac agtcagaata 3041 gttattctct aagaggaaac tagtgtttgt taaaaacaaa aataaaaaca aaaccacaca 3101 aggagaaccc aattttgttt caacaatttt tgatcaatgt atatgaagct cttgatagga 3161 cttccttaag catgacggga aaaccaaaca cgttccctaa tcaggaaaaa aaaaaaaaaa 3221 aaaaagtaag acacaaacaa accatttttt tctctttttt tggagttggg ggcccaggga 3281 gaagggacaa ggcttttaaa agacttgtta gccaacttca agaattaata tttatgtctc 3341 tgttattgtt agttttaagc cttaaggtag aaggcacata gaaataacat c 3392 4 18 DNA Artificial Sequence PCR Primer 4 cgtgggctac cgcatttc 18 5 22 DNA Artificial Sequence PCR Primer 5 tcatcatcac catcaggatt cc 22 6 27 DNA Artificial Sequence PCR Probe 6 tccaacgtgg atgtggcctt actatgg 27 7 19 DNA Artificial Sequence PCR Primer 7 gaaggtgaag gtcggagtc 19 8 20 DNA Artificial Sequence PCR Primer 8 gaagatggtg atgggatttc 20 9 20 DNA Artificial Sequence PCR Probe 9 caagcttccc gttctcagcc 20 10 2878 DNA Mus musculus CDS (25)...(2709) 10 ctggatgtgg cagagggagc cagc atg atc ctc ttg gca gtg ctt ttt ct c 51 Met Ile Leu Leu Ala Val Leu Phe Leu 1 5 tgc ttc ttc tcc tcc tac tct gct tcc gtt aaa ggt cac aca act g gc 99 Cys Phe Phe Ser Ser Tyr Ser Ala Ser Val Lys Gly His Thr Thr Gly 10 15 20 25 ctc tca tta aat aat gag cgg cta tac aag ctc acg tac tcc act ga a 147 Leu Ser Leu Asn Asn Glu Arg Leu Tyr Lys Leu Thr Tyr Ser Thr Glu 30 35 40 gtg ttt ctt gat ggg ggc aaa gga aaa ccg caa gac agc gtg ggc tac 195 Val Phe Leu Asp Gly Gly Lys Gly Lys Pro Gln Asp Ser Val Gly Tyr 45 50 55 aaa atc tca tct gat gtg gac gtt gtg tta ctg tgg agg aat cct gat 243 Lys Ile Ser Ser Asp Val Asp Val Val Leu Leu Trp Arg Asn Pro Asp 60 65 70 ggt gat gat gat caa gtg atc caa gtc acg ata aca gct gtt aac gtt 291 Gly Asp Asp Asp Gln Val Ile Gln Val Thr Ile Thr Ala Val Asn Val 75 80 85 gaa aat gcg ggt caa cag aga ggc gag aag agc atc ttc cag ggc aaa 339 Glu Asn Ala Gly Gln Gln Arg Gly Glu Lys Ser Ile Phe Gln Gly Lys 90 95 100 105 agt aca cct aag atc ata ggg aag gac aac ctg gag gct ctg cag aga 387 Ser Thr Pro Lys Ile Ile Gly Lys Asp Asn Leu Glu Ala Leu Gln Arg 110 115 120 ccc atg ctt ctt cat ctg gtc cgg ggg aag gtc aag gag ttc tac tcc 435 Pro Met Leu Leu His Leu Val Arg Gly Lys Val Lys Glu Phe Tyr Ser 125 130 135 tat gaa aac gag cca gtg ggc ata gaa aat ctc aag aga ggc ttg gct 483 Tyr Glu Asn Glu Pro Val Gly Ile Glu Asn Leu Lys Arg Gly Leu Ala 140 145 150 agc tta ttc cag atg cag cta agc tct gga act acc aac gag gta gat 531 Ser Leu Phe Gln Met Gln Leu Ser Ser Gly Thr Thr Asn Glu Val Asp 155 160 165 atc tct ggg gat tgt aaa gtg acc tac cag gcc caa caa gac aaa gtg 579 Ile Ser Gly Asp Cys Lys Val Thr Tyr Gln Ala Gln Gln Asp Lys Val 170 175 180 185 gtc aaa att aag gct ctg gat aca tgc aaa att gag cgg tct gga ttt 627 Val Lys Ile Lys Ala Leu Asp Thr Cys Lys Ile Glu Arg Ser Gly Phe 190 195 200 aca acg gca aac cag gtg ctg ggc gtc agt tca aaa gcc aca tct gtc 675 Thr Thr Ala Asn Gln Val Leu Gly Val Ser Ser Lys Ala Thr Ser Val 205 210 215 act acc tac aag ata gag gac agc ttt gtc acc gct gtg ctt gca gaa 723 Thr Thr Tyr Lys Ile Glu Asp Ser Phe Val Thr Ala Val Leu Ala Glu 220 225 230 gag acc agg gct ttt gcc ttg aac ttc caa caa acc ata gca gga aaa 771 Glu Thr Arg Ala Phe Ala Leu Asn Phe Gln Gln Thr Ile Ala Gly Lys 235 240 245 ata gtg tca aag cag aaa ttg gag ctg aag aca act gaa gcc ggc cca 819 Ile Val Ser Lys Gln Lys Leu Glu Leu Lys Thr Thr Glu Ala Gly Pro 250 255 260 265 agg atg atc ccc ggg aag caa gtg gca ggt gta att aaa gca gtt gat 867 Arg Met Ile Pro Gly Lys Gln Val Ala Gly Val Ile Lys Ala Val Asp 270 275 280 tcc aaa tac aaa gcc att ccc att gtg gga cag gtc ctc gag cgt gtc 915 Ser Lys Tyr Lys Ala Ile Pro Ile Val Gly Gln Val Leu Glu Arg Val 285 290 295 tgc aaa gga tgc cct tct ctg gcg gag cac tgg aag tcc atc aga aag 963 Cys Lys Gly Cys Pro Ser Leu Ala Glu His Trp Lys Ser Ile Arg Lys 300 305 310 aac ctg gag cct gaa aac ctg tcc aag gcc gag gct gtc cag agc ttc 1011 Asn Leu Glu Pro Glu Asn Leu Ser Lys Ala Glu Ala Val Gln Ser Phe 315 320 325 ctg gcc ttc atc cag cac ctc cgg act tcg agg aga gaa gag atc ctc 1059 Leu Ala Phe Ile Gln His Leu Arg Thr Ser Arg Arg Glu Glu Ile Leu 330 335 340 345 cag att ctg aag gca gag aag aaa gaa gtg ctc cct cag ctg gtg gat 1107 Gln Ile Leu Lys Ala Glu Lys Lys Glu Val Leu Pro Gln Leu Val Asp 350 355 360 gcc gtc acc tct gct cag act cca gac tcg cta gaa gcc atc ctg gac 1155 Ala Val Thr Ser Ala Gln Thr Pro Asp Ser Leu Glu Ala Ile Leu Asp 365 370 375 ttt ttg gat ttc aaa agt gac agc agt atc ata ctc cag gaa agg ttc 1203 Phe Leu Asp Phe Lys Ser Asp Ser Ser Ile Ile Leu Gln Glu Arg Phe 380 385 390 ctc tat gcc tgt ggc ttt gcc acc cac cct gat gaa gaa ctc cta cga 1251 Leu Tyr Ala Cys Gly Phe Ala Thr His Pro Asp Glu Glu Leu Leu Arg 395 400 405 gcc ctc ctt agt aag ttc aaa ggt tcc ttt gca agc aac gac atc aga 1299 Ala Leu Leu Ser Lys Phe Lys Gly Ser Phe Ala Ser Asn Asp Ile Arg 410 415 420 425 gag tcg gtt atg atc atc att gga gcc cta gtc agg aag ctg tgt cag 1347 Glu Ser Val Met Ile Ile Ile Gly Ala Leu Val Arg Lys Leu Cys Gln 430 435 440 aat gaa ggc tgc aag ctc aag gca gtg gtg gaa gct aag aag ctg atc 1395 Asn Glu Gly Cys Lys Leu Lys Ala Val Val Glu Ala Lys Lys Leu Ile 445 450 455 ctg gga gga ctt gaa aaa cca gag aag aaa gaa gac acc aca atg tac 1443 Leu Gly Gly Leu Glu Lys Pro Glu Lys Lys Glu Asp Thr Thr Met Tyr 460 465 470 ctg ctg gcc ctg aag aat gcc ttg ctt ccc gaa ggc atc ccg ctc ctt 1491 Leu Leu Ala Leu Lys Asn Ala Leu Leu Pro Glu Gly Ile Pro Leu Leu 475 480 485 ctg aag tat gct gag gct gga gaa ggg ccc gtc agc cac ctg gcc acc 1539 Leu Lys Tyr Ala Glu Ala Gly Glu Gly Pro Val Ser His Leu Ala Thr 490 495 500 505 act gtt ctc cag aga tac gat gtc tcc ttc atc aca gat gag gtg aag 1587 Thr Val Leu Gln Arg Tyr Asp Val Ser Phe Ile Thr Asp Glu Val Lys 510 515 520 aag acc ttg aac agg ata tac cac cag aat cgt aag gtt cat gag aag 1635 Lys Thr Leu Asn Arg Ile Tyr His Gln Asn Arg Lys Val His Glu Lys 525 530 535 acg gtg cgc aca act gcc gct gct gtc atc tta aag aac cca tcc tac 1683 Thr Val Arg Thr Thr Ala Ala Ala Val Ile Leu Lys Asn Pro Ser Tyr 540 545 550 atg gat gtg aag aac atc ctg ctg tcc att ggg gaa ctc ccg aaa gag 1731 Met Asp Val Lys Asn Ile Leu Leu Ser Ile Gly Glu Leu Pro Lys Glu 555 560 565 atg aac aaa tac atg ctc acc gtt gtg caa gac atc ctg cat ttt gaa 1779 Met Asn Lys Tyr Met Leu Thr Val Val Gln Asp Ile Leu His Phe Glu 570 575 580 585 atg cct gca agc aaa atg atc cgt cga gtt ctc aag gag atg gct gtt 1827 Met Pro Ala Ser Lys Met Ile Arg Arg Val Leu Lys Glu Met Ala Val 590 595 600 cac aat tat gac cgt ttc tcc aag agt gga tcc tct tct gcc tat act 1875 His Asn Tyr Asp Arg Phe Ser Lys Ser Gly Ser Ser Ser Ala Tyr Thr 605 610 615 ggc tac gta gaa cgt agc ccc cgt gca gcg tcc aca tac agc ctt gac 1923 Gly Tyr Val Glu Arg Ser Pro Arg Ala Ala Ser Thr Tyr Ser Leu Asp 620 625 630 atc ctt tac tct ggc tct ggc att ctg agg aga agt aac ctg aac atc 1971 Ile Leu Tyr Ser Gly Ser Gly Ile Leu Arg Arg Ser Asn Leu Asn Ile 635 640 645 ttc cag tac atc aaa gga aca gag ctt cat ggt agt cag gtg gtg att 2019 Phe Gln Tyr Ile Lys Gly Thr Glu Leu His Gly Ser Gln Val Val Ile 650 655 660 665 gaa gcc caa ggg ctg gaa ggc tta att gca gcc act cct gat gaa gga 2067 Glu Ala Gln Gly Leu Glu Gly Leu Ile Ala Ala Thr Pro Asp Glu Gly 670 675 680 gag gag aac ctt gac tct tat gct ggc atg tca gcc atc ctg ttt gat 2115 Glu Glu Asn Leu Asp Ser Tyr Ala Gly Met Ser Ala Ile Leu Phe Asp 685 690 695 gtt cag ctt agg cct gtc aca ttt ttt aat gga tac agt gat ttg atg 2163 Val Gln Leu Arg Pro Val Thr Phe Phe Asn Gly Tyr Ser Asp Leu Met 700 705 710 tcc aaa atg ctg tcg gca tcc ggc gac cct gtc agc gtg gtg aaa ggg 2211 Ser Lys Met Leu Ser Ala Ser Gly Asp Pro Val Ser Val Val Lys Gly 715 720 725 ctt att ctg tta ata gac cat tct cag gat att cag ctg caa tct gga 2259 Leu Ile Leu Leu Ile Asp His Ser Gln Asp Ile Gln Leu Gln Ser Gly 730 735 740 745 cta aag gcc aat atg gag atc cag ggt ggt cta gct att gat att tct 2307 Leu Lys Ala Asn Met Glu Ile Gln Gly Gly Leu Ala Ile Asp Ile Ser 750 755 760 ggt tca atg gaa ttc agt ctg tgg tat cgc gag tct aaa acc cga gtg 2355 Gly Ser Met Glu Phe Ser Leu Trp Tyr Arg Glu Ser Lys Thr Arg Val 765 770 775 aaa aat cgg gtg gct gtg gtg ata acc agc gac gtc aca gtg gat gcc 2403 Lys Asn Arg Val Ala Val Val Ile Thr Ser Asp Val Thr Val Asp Ala 780 785 790 tct ttt gtg aaa gct ggt ctg gaa agc aga gcg gag aca gag gct ggg 2451 Ser Phe Val Lys Ala Gly Leu Glu Ser Arg Ala Glu Thr Glu Ala Gly 795 800 805 ctg gag ttc atc tcc aca gtg cag ttc tca cag tac ccg ttc ttg gtc 2499 Leu Glu Phe Ile Ser Thr Val Gln Phe Ser Gln Tyr Pro Phe Leu Val 810 815 820 825 tgc atg cag atg gac aag gct gaa gcc cca ctc agg caa ttc gag aca 2547 Cys Met Gln Met Asp Lys Ala Glu Ala Pro Leu Arg Gln Phe Glu Thr 830 835 840 aag tat gaa agg cta tct aca ggc agg gga tat gtc tct cgg aga aga 2595 Lys Tyr Glu Arg Leu Ser Thr Gly Arg Gly Tyr Val Ser Arg Arg Arg 845 850 855 aaa gag agc cta gtg gcc gga tgt gaa ctc ccc ctc cat caa cag aac 2643 Lys Glu Ser Leu Val Ala Gly Cys Glu Leu Pro Leu His Gln Gln Asn 860 865 870 tct gag atg tgc aac gtg gta ttc cca cct cag cca gaa agc gat aac 2691 Ser Glu Met Cys Asn Val Val Phe Pro Pro Gln Pro Glu Ser Asp Asn 875 880 885 tcc ggt gga tgg ttt tga ttcccgtggg ttcccttcca ccagaacgat 2739 Ser Gly Gly Trp Phe 890 atgctatgac gtgcctgacc cttgctctct gagagcacag tgtttacata tttacctgta 2799 tttaagatgt ttgtaaagag cagtggagaa cttcagttga ttaaagttga acctattcag 2859 gagaagaccc acagtgtcc 2878 11 18 DNA Artificial Sequence PCR Primer 11 gagcggtctg gatttaca 18 12 24 DNA Artificial Sequence PCR Primer 12 aggtagtgac agatgtggct tttg 24 13 23 DNA Artificial Sequence PCR Probe 13 caaaccaggt gctgggcgtc agt 23 14 20 DNA Artificial Sequence PCR Primer 14 ggcaaattca acggcacagt 20 15 20 DNA Artificial Sequence PCR Primer 15 gggtctcgct cctggaagat 20 16 27 DNA Artificial Sequence PCR Probe 16 aaggccgaga atgggaagct tgtcatc 27 17 20 DNA Artificial Sequence Antisense Oligonucleotide 17 cagtgcccag ctaggagtca 20 18 20 DNA Artificial Sequence Antisense Oligonucleotide 18 tcaactgcat ccagtgccca 20 19 20 DNA Artificial Sequence Antisense Oligonucleotide 19 tcatattgac cagcaatcct 20 20 20 DNA Artificial Sequence Antisense Oligonucleotide 20 ccagttgtgt gacctttaac 20 21 20 DNA Artificial Sequence Antisense Oligonucleotide 21 acgtgagctt gtacagccgg 20 22 20 DNA Artificial Sequence Antisense Oligonucleotide 22 gcggtagccc acgctgtctt 20 23 20 DNA Artificial Sequence Antisense Oligonucleotide 23 gattcctcca tagtaaggcc 20 24 20 DNA Artificial Sequence Antisense Oligonucleotide 24 gattagatga aggagcgtag 20 25 20 DNA Artificial Sequence Antisense Oligonucleotide 25 gtggttccag agcttaactg 20 26 20 DNA Artificial Sequence Antisense Oligonucleotide 26 aggtggtgac agatgtagct 20 27 20 DNA Artificial Sequence Antisense Oligonucleotide 27 gctgcagcct gctttccaga 20 28 20 DNA Artificial Sequence Antisense Oligonucleotide 28 acagtggctc tggaagacct 20 29 20 DNA Artificial Sequence Antisense Oligonucleotide 29 tggtggaccg ccagagctcc 20 30 20 DNA Artificial Sequence Antisense Oligonucleotide 30 gaggtgacag catccaccag 20 31 20 DNA Artificial Sequence Antisense Oligonucleotide 31 atggcttcta atgagtctga 20 32 20 DNA Artificial Sequence Antisense Oligonucleotide 32 cctggaggat aatgctgctg 20 33 20 DNA Artificial Sequence Antisense Oligonucleotide 33 agtgtcccag tgatgatcat 20 34 20 DNA Artificial Sequence Antisense Oligonucleotide 34 agcagataca tcctggtgtc 20 35 20 DNA Artificial Sequence Antisense Oligonucleotide 35 cccttctcct gcttctgcat 20 36 20 DNA Artificial Sequence Antisense Oligonucleotide 36 gagcagtggt agccaggtgg 20 37 20 DNA Artificial Sequence Antisense Oligonucleotide 37 taaggtcttc ttcacctcat 20 38 20 DNA Artificial Sequence Antisense Oligonucleotide 38 gcagctgcag cagtgcgcac 20 39 20 DNA Artificial Sequence Antisense Oligonucleotide 39 cttgacgtcc atgtaggatg 20 40 20 DNA Artificial Sequence Antisense Oligonucleotide 40 ctatgtagcc agtgtaggca 20 41 20 DNA Artificial Sequence Antisense Oligonucleotide 41 cgagtagaga atgtctaggc 20 42 20 DNA Artificial Sequence Antisense Oligonucleotide 42 taccgtgaag accagccttc 20 43 20 DNA Artificial Sequence Antisense Oligonucleotide 43 attaaggctt ccagtccttg 20 44 20 DNA Artificial Sequence Antisense Oligonucleotide 44 ccctggacct ctatattggc 20 45 20 DNA Artificial Sequence Antisense Oligonucleotide 45 gataccacaa gctaaactcc 20 46 20 DNA Artificial Sequence Antisense Oligonucleotide 46 gaggagtcca ctgtgatgtc 20 47 20 DNA Artificial Sequence Antisense Oligonucleotide 47 gtactggttt ccaggccagc 20 48 20 DNA Artificial Sequence Antisense Oligonucleotide 48 gcttcatcct tgtccatctg 20 49 20 DNA Artificial Sequence Antisense Oligonucleotide 49 cgctggaagt actatccggc 20 50 20 DNA Artificial Sequence Antisense Oligonucleotide 50 aatatcacag gtcagtttca 20 51 20 DNA Artificial Sequence Antisense Oligonucleotide 51 catgccacat tgtgtccctt 20 52 20 DNA Artificial Sequence Antisense Oligonucleotide 52 cgctgtgctc tcagagagca 20 53 20 DNA Artificial Sequence Antisense Oligonucleotide 53 gtagcatact gcatataccc 20 54 20 DNA Artificial Sequence Antisense Oligonucleotide 54 gatgattcaa aatgacgctg 20 55 20 DNA Artificial Sequence Antisense Oligonucleotide 55 gatttgagag aggtataagt 20 56 20 DNA Artificial Sequence Antisense Oligonucleotide 56 gagaataact attctgactg 20 57 20 DNA Artificial Sequence Antisense Oligonucleotide 57 gagcttcata tacattgatc 20 58 20 DNA Artificial Sequence Antisense Oligonucleotide 58 cccgtcatgc ttaaggaagt 20 59 20 DNA Artificial Sequence Antisense Oligonucleotide 59 atgtgccttc taccttaagg 20 60 20 DNA Artificial Sequence Antisense Oligonucleotide 60 gctccctctg ccacatccag 20 61 20 DNA Artificial Sequence Antisense Oligonucleotide 61 gatcatgctg gctccctctg 20 62 20 DNA Artificial Sequence Antisense Oligonucleotide 62 gagtacgtga gcttgtatag 20 63 20 DNA Artificial Sequence Antisense Oligonucleotide 63 gtagcccacg ctgtcttgcg 20 64 20 DNA Artificial Sequence Antisense Oligonucleotide 64 catcaccatc aggattcctc 20 65 20 DNA Artificial Sequence Antisense Oligonucleotide 65 gccctggaag atgctcttct 20 66 20 DNA Artificial Sequence Antisense Oligonucleotide 66 gcctccaggt tgtccttccc 20 67 20 DNA Artificial Sequence Antisense Oligonucleotide 67 tagaactcct tgaccttccc 20 68 20 DNA Artificial Sequence Antisense Oligonucleotide 68 tggaataagc tagccaagcc 20 69 20 DNA Artificial Sequence Antisense Oligonucleotide 69 cccagagata tctacctcgt 20 70 20 DNA Artificial Sequence Antisense Oligonucleotide 70 cccagcacct ggtttgccgt 20 71 20 DNA Artificial Sequence Antisense Oligonucleotide 71 ccctggtctc ttctgcaagc 20 72 20 DNA Artificial Sequence Antisense Oligonucleotide 72 cacctgccac ttgcttcccg 20 73 20 DNA Artificial Sequence Antisense Oligonucleotide 73 gctcgaggac ctgtcccaca 20 74 20 DNA Artificial Sequence Antisense Oligonucleotide 74 ttccagtgct ccgccagaga 20 75 20 DNA Artificial Sequence Antisense Oligonucleotide 75 gaagtccgga ggtgctggat 20 76 20 DNA Artificial Sequence Antisense Oligonucleotide 76 cagaggtgac ggcatccacc 20 77 20 DNA Artificial Sequence Antisense Oligonucleotide 77 cctggagtat gatactgctg 20 78 20 DNA Artificial Sequence Antisense Oligonucleotide 78 ctctgatgtc gttgcttgca 20 79 20 DNA Artificial Sequence Antisense Oligonucleotide 79 attctgacac agcttcctga 20 80 20 DNA Artificial Sequence Antisense Oligonucleotide 80 cccaggatca gcttcttagc 20 81 20 DNA Artificial Sequence Antisense Oligonucleotide 81 cagcctcagc atacttcaga 20 82 20 DNA Artificial Sequence Antisense Oligonucleotide 82 gtggctgacg ggcccttctc 20 83 20 DNA Artificial Sequence Antisense Oligonucleotide 83 acgattctgg tggtatatcc 20 84 20 DNA Artificial Sequence Antisense Oligonucleotide 84 cagcagcggc agttgtgcgc 20 85 20 DNA Artificial Sequence Antisense Oligonucleotide 85 tgcacaacgg tgagcatgta 20 86 20 DNA Artificial Sequence Antisense Oligonucleotide 86 gccagtatag gcagaagagg 20 87 20 DNA Artificial Sequence Antisense Oligonucleotide 87 aaggctgtat gtggacgctg 20 88 20 DNA Artificial Sequence Antisense Oligonucleotide 88 cagaatgcca gagccagagt 20 89 20 DNA Artificial Sequence Antisense Oligonucleotide 89 ctgcaattaa gccttccagc 20 90 20 DNA Artificial Sequence Antisense Oligonucleotide 90 ctctccttca tcaggagtgg 20 91 20 DNA Artificial Sequence Antisense Oligonucleotide 91 tgacatgcca gcataagagt 20 92 20 DNA Artificial Sequence Antisense Oligonucleotide 92 cgctgacagg gtcgccggat 20 93 20 DNA Artificial Sequence Antisense Oligonucleotide 93 ccctttcacc acgctgacag 20 94 20 DNA Artificial Sequence Antisense Oligonucleotide 94 gaccaccctg gatctccata 20 95 20 DNA Artificial Sequence Antisense Oligonucleotide 95 ctcgcgatac cacagactga 20 96 20 DNA Artificial Sequence Antisense Oligonucleotide 96 gttatcacca cagccacccg 20 97 20 DNA Artificial Sequence Antisense Oligonucleotide 97 gaactccagc ccagcctctg 20 98 20 DNA Artificial Sequence Antisense Oligonucleotide 98 agccttgtcc atctgcatgc 20 99 20 DNA Artificial Sequence Antisense Oligonucleotide 99 cacatccggc cactaggctc 20 100 20 DNA Artificial Sequence Antisense Oligonucleotide 100 tctcagagtt ctgttgatgg 20 101 20 DNA Artificial Sequence Antisense Oligonucleotide 101 cgtcatagca tatcgttctg 20 102 20 DNA Artificial Sequence Antisense Oligonucleotide 102 actgtgctct cagagagcaa 20 103 20 DNA Artificial Sequence Antisense Oligonucleotide 103 ggtcttctcc tgaataggtt 20 104 20 DNA Artificial Sequence Antisense Oligonucleotide 104 ggccagttgt gtgaccttta 20 105 20 DNA Artificial Sequence Antisense Oligonucleotide 105 catcaagaaa cacttcagtg 20 106 20 DNA Artificial Sequence Antisense Oligonucleotide 106 caacgtccac atcagatgag 20 107 20 DNA Artificial Sequence Antisense Oligonucleotide 107 ctgttatcgt gacttggatc 20 108 20 DNA Artificial Sequence Antisense Oligonucleotide 108 gaagaagcat gggtctctgc 20 109 20 DNA Artificial Sequence Antisense Oligonucleotide 109 ctatgcccac tggctcgttt 20 110 20 DNA Artificial Sequence Antisense Oligonucleotide 110 tggtagttcc agagcttagc 20 111 20 DNA Artificial Sequence Antisense Oligonucleotide 111 tggtaggtca ctttacaatc 20 112 20 DNA Artificial Sequence Antisense Oligonucleotide 112 atgtggcttt tgaactgacg 20 113 20 DNA Artificial Sequence Antisense Oligonucleotide 113 tatcttgtag gtagtgacag 20 114 20 DNA Artificial Sequence Antisense Oligonucleotide 114 gcggtgacaa agctgtcctc 20 115 20 DNA Artificial Sequence Antisense Oligonucleotide 115 gggcatcctt tgcagacacg 20 116 20 DNA Artificial Sequence Antisense Oligonucleotide 116 cagcctcggc cttggacagg 20 117 20 DNA Artificial Sequence Antisense Oligonucleotide 117 gaaggccagg aagctctgga 20 118 20 DNA Artificial Sequence Antisense Oligonucleotide 118 tagcgagtct ggagtctgag 20 119 20 DNA Artificial Sequence Antisense Oligonucleotide 119 aatgatgatc ataaccgact 20 120 20 DNA Artificial Sequence Antisense Oligonucleotide 120 gccttgagct tgcagccttc 20 121 20 DNA Artificial Sequence Antisense Oligonucleotide 121 ccagcaggta cattgtggtg 20 122 20 DNA Artificial Sequence Antisense Oligonucleotide 122 tgaaggagac atcgtatctc 20 123 20 DNA Artificial Sequence Antisense Oligonucleotide 123 accgtcttct catgaacctt 20 124 20 DNA Artificial Sequence Antisense Oligonucleotide 124 atgttcttca catccatgta 20 125 20 DNA Artificial Sequence Antisense Oligonucleotide 125 atctccttga gaactcgacg 20 126 20 DNA Artificial Sequence Antisense Oligonucleotide 126 ggtcataatt gtgaacagcc 20 127 20 DNA Artificial Sequence Antisense Oligonucleotide 127 caatcaccac ctgactacca 20 128 20 DNA Artificial Sequence Antisense Oligonucleotide 128 tgaacatcaa acaggatggc 20 129 20 DNA Artificial Sequence Antisense Oligonucleotide 129 ggtctattaa cagaataagc 20 130 20 DNA Artificial Sequence Antisense Oligonucleotide 130 cagctgaata tcctgagaat 20 131 20 DNA Artificial Sequence Antisense Oligonucleotide 131 gggttttaga ctcgcgatac 20 132 20 DNA Artificial Sequence Antisense Oligonucleotide 132 atccactgtg acgtcgctgg 20 133 20 DNA Artificial Sequence Antisense Oligonucleotide 133 gagaactgca ctgtggagat 20 134 20 DNA Artificial Sequence Antisense Oligonucleotide 134 ctgcctgtag atagcctttc 20 135 20 DNA Artificial Sequence Antisense Oligonucleotide 135 tgggaatacc acgttgcaca 20 136 20 DNA Artificial Sequence Antisense Oligonucleotide 136 atacaggtaa atatgtaaac 20 137 20 DNA Artificial Sequence Antisense Oligonucleotide 137 atcaactgaa gttctccact 20 

What is claimed is:
 1. A compound 8 to 50 nucleobases in length targeted to a nucleic acid molecule encoding microsomal triglyceride transfer protein, wherein said compound specifically hybridizes with and inhibits the expression of a nucleic aid molecule encoding microsomal triglyceride transfer protein.
 2. The compound of claim 1 which is an antisense oligonucleotide.
 3. The compound of claim 2 wherein the antisense oligonucleotide has a sequence comprising SEQ ID NO: 17, 18, 19, 20, 22, 23, 32, 33, 47, 48, 49, 50, 51, 52, 53, 54, 57, 58, 59, 70, 71, 72, 73, 74, 77, 78, 79, 81, 82, 85, 88, 89, 91, 92, 93, 94, 95, 96, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136,
 137. 4. The compound of claim 2 wherein the antisense oligonucleotide comprises at least one modified internucleoside linkage.
 5. The compound of claim 4 wherein the modified internucleoside linkage is a phosphorothioate linkage.
 6. The compound of claim 2 wherein the antisense oligonucleotide comprises at least one modified sugar moiety.
 7. The compound of claim 6 wherein the modified sugar moiety is a 2′-O-methoxyethyl sugar moiety.
 8. The compound of claim 2 wherein the antisense oligonucleotide comprises at least one modified nucleobase.
 9. The compound of claim 8 wherein the modified nucleobase is a 5-methylcytosine.
 10. The compound of claim 2 wherein the antisense oligonucleotide is a chimeric oligonucleotide.
 11. A compound 8 to 50 nucleobases in length which specifically hybridizes with at least an 8-nucleobase portion of an active site on a nucleic acid molecule encoding microsomal triglyceride transfer protein.
 12. A composition comprising the compound of claim 1 and a pharmaceutically acceptable carrier or diluent.
 13. The composition of claim 12 further comprising a colloidal dispersion system.
 14. The composition of claim 12 wherein the compound is an antisense oligonucleotide.
 15. A method of inhibiting the expression of microsomal triglyceride transfer protein in cells or tissues comprising contacting said cells or tissues with the compound of claim 1 so that expression of microsomal triglyceride transfer protein is inhibited.
 16. A method of treating an animal having a disease or condition associated with microsomal triglyceride transfer protein comprising administering to said animal a therapeutically or prophylactically effective amount of the compound of claim 1 so that expression of microsomal triglyceride transfer protein is inhibited.
 17. The method of claim 16 wherein the condition involves abnormal lipid metabolism.
 18. The method of claim 16 wherein the condition involves abnormal cholesterol metabolism.
 19. The method of claim 16 wherein the condition is atherosclerosis.
 20. The method of claim 16 wherein the disease is cardiovascular disease. 